Tandem Repeats Finder Program written by:
Gary Benson
Program in Bioinformatics
Boston University
Version 4.09
Sequence: At_chr12
Parameters: 2 7 7 80 10 50 1000
Pmatch=0.80,Pindel=0.10
tuple sizes 0,4,5,7
tuple distances 0, 29, 159, 1000
Length: 101062743
ACGTcount: A:0.31, C:0.17, G:0.17, T:0.31
Warning! 4026412 characters in sequence are not A, C, G, or T
File 78 of 297
Found at i:27809823 original size:47 final size:47
Alignment explanation
Indices: 27809709--27809980 Score: 265
Period size: 46 Copynumber: 5.8 Consensus size: 47
27809699 TAACTTATGT
* *
27809709 GAGCCAGTGTAAGAAC-TGTCTGGGACATGCATCGGCCACTT--TATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGG-CA-TTGAGATGA
* * *
27809755 GAGCCAGTATAAGACCGTGTCTGGGACATGGCATCGGCATTGAGACGA
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGATGA
* * * *
27809803 GAGCTAGTGTAAGA-CATGTCTGGGACATGCATCAGCCTCGAGATGTA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCATTGAGATG-A
*
27809850 -AGCCAGTGTAAGA-CATGTCTGGGACATGCATCGGC-TACGAGATGA
1 GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCAT-TGAGATGA
* * * *
27809895 TAGTCAGTGTAAGACCGTGTCTGGGACATGGCATCGAC-TTGAGAT-A
1 GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCATTGAGATGA
* *
27809941 TGAGCCAGTGTAAGACCGTGTCTAGGACATGGCATCGGCA
1 -GAGCCAGTGTAAGACCATGTCTGGGACAT-GCATCGGCA
27809981 CCTTACCCAC
Statistics
Matches: 194, Mismatches: 21, Indels: 20
0.83 0.09 0.09
Matches are distributed among these distances:
45 2 0.01
46 82 0.42
47 80 0.41
48 30 0.15
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.22
Consensus pattern (47 bp):
GAGCCAGTGTAAGACCATGTCTGGGACATGCATCGGCATTGAGATGA
Found at i:27809963 original size:140 final size:141
Alignment explanation
Indices: 27809705--27809976 Score: 372
Period size: 140 Copynumber: 1.9 Consensus size: 141
27809695 TGGGTAACTT
* ***
27809705 ATGTGAGCCAGTGTAAGAACTGTCTGGGACATGCATCGGCCACTTTATGAGAGCCAGTATAAGAC
1 ATGTAAGCCAGTGTAAGAACTGTCTGGGACATGCATCGGCCACGAGATGAGAGCCAGTATAAGAC
* * *
27809770 CGTGTCTGGGACATGGCATCGGCATTGAGACGAGAGCTAGTGTAAGACATGTCTGGGACAT-GCA
66 CGTGTCTGGGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTAGGACATGGCA
27809834 TCAGCCTCGAG
131 TCAGCCTCGAG
* * * *
27809845 ATGTAAGCCAGTGTAAG-ACATGTCTGGGACATGCATCGGCTACGAGATGATAGTCAGTGTAAGA
1 ATGTAAGCCAGTGTAAGAAC-TGTCTGGGACATGCATCGGCCACGAGATGAGAGCCAGTATAAGA
* *
27809909 CCGTGTCTGGGACATGGCATCGAC-TTGAGA-TATGAGCCAGTGTAAGACCGTGTCTAGGACATG
65 CCGTGTCTGGGACATGGCATCGACATTGAGACGA-GAGCCAGTGTAAGA-CATGTCTAGGACATG
27809972 GCATC
128 GCATC
27809977 GGCACCTTAC
Statistics
Matches: 115, Mismatches: 13, Indels: 7
0.85 0.10 0.05
Matches are distributed among these distances:
138 1 0.01
139 21 0.18
140 88 0.77
141 5 0.04
ACGTcount: A:0.27, C:0.20, G:0.31, T:0.23
Consensus pattern (141 bp):
ATGTAAGCCAGTGTAAGAACTGTCTGGGACATGCATCGGCCACGAGATGAGAGCCAGTATAAGAC
CGTGTCTGGGACATGGCATCGACATTGAGACGAGAGCCAGTGTAAGACATGTCTAGGACATGGCA
TCAGCCTCGAG
Found at i:27813632 original size:79 final size:81
Alignment explanation
Indices: 27813496--27813678 Score: 232
Period size: 79 Copynumber: 2.3 Consensus size: 81
27813486 TCGAATGATG
* *
27813496 TCCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATATCCGGACTAAGATCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
27813560 TGTGCGAGTTACTA-A
66 TGTGCGAGTTACTATA
* * * **
27813575 TTCCGGGCTAAG-CCCGAAGGCATTGGTGC-GAGTTACTAAATCCGGGTTAAG-TCCCGAAGGCA
1 -TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGAT-CCGAAGGCA
27813637 TTTGTGCGAGTTACTATA
64 TTTGTGCGAGTTACTATA
* *
27813655 ACCGGGCTATGTCCCGAAGGCATT
1 TCCGGGCTAAGTCCCGAAGGCATT
27813679 TGAACGAGTA
Statistics
Matches: 90, Mismatches: 9, Indels: 8
0.84 0.08 0.07
Matches are distributed among these distances:
78 1 0.01
79 59 0.66
80 30 0.33
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (81 bp):
TCCGGGCTAAGTCCCGAAGGCATTGGTGCTAAGTGACCAAATCCGGACTAAGATCCGAAGGCATT
TGTGCGAGTTACTATA
Found at i:27813694 original size:40 final size:40
Alignment explanation
Indices: 27813497--27813680 Score: 216
Period size: 40 Copynumber: 4.6 Consensus size: 40
27813487 CGAATGATGT
* * * *
27813497 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACCATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTATAA
* *
27813537 CCGGACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTA-ATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTATA-A
*
27813577 CCGGGCTAAG-CCCGAAGGCATTGGTGCGAGTTACTA-AA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
27813615 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
*
27813656 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
27813681 AACGAGTAGC
Statistics
Matches: 126, Mismatches: 11, Indels: 14
0.83 0.07 0.09
Matches are distributed among these distances:
39 35 0.28
40 81 0.64
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.28, T:0.25
Consensus pattern (40 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
Found at i:27813702 original size:79 final size:79
Alignment explanation
Indices: 27813549--27813713 Score: 210
Period size: 79 Copynumber: 2.1 Consensus size: 79
27813539 GGACTAAGAT
* **
27813549 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGGCTAAGCCCGAAGGCATTGGTGCGAGTTACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
*
27813614 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* *
27813628 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAG-TAGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGGCTAAG-CCCGAAGGCATTGGAACGAGTTA-C
* *
27813691 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
27813707 CCGAAGG
1 CCGAAGG
27813714 TACGTGATTC
Statistics
Matches: 75, Mismatches: 8, Indels: 6
0.84 0.09 0.07
Matches are distributed among these distances:
78 2 0.03
79 49 0.65
80 24 0.32
ACGTcount: A:0.25, C:0.21, G:0.28, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGGCTAAGCCCGAAGGCATTGGAACGAGTTACTAA
ATCCGGGTTAAATC
Found at i:27821861 original size:40 final size:39
Alignment explanation
Indices: 27821671--27821854 Score: 194
Period size: 40 Copynumber: 4.6 Consensus size: 39
27821661 CGAATGATGT
* * *
27821671 CCGGGCTAAGTCCCGAAGGC-TTTGTGCTAAGTGACTATAT
1 CCGGGCTAAGTCCCGAAGGCATTTGTGC-GAGTTACTA-AA
** *
27821711 CCGAACTAAGAT-CCGAAGGCATTTGTGCGAGTTACTAATT
1 CCGGGCTAAG-TCCCGAAGGCATTTGTGCGAGTTACTAA-A
* * *
27821751 CCGGCCTAAG-CCCGAAGGCATTGGTGCGAGTCACTAAA
1 CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
*
27821789 TCCGGGTTAAGTCCCGAAGGCATTTGTGCGAGTTACTATAA
1 -CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTA-AA
*
27821830 CCGGGCTATGTCCCGAAGGCATTTG
1 CCGGGCTAAGTCCCGAAGGCATTTG
27821855 AACGAGTAGC
Statistics
Matches: 122, Mismatches: 15, Indels: 14
0.81 0.10 0.09
Matches are distributed among these distances:
39 33 0.27
40 79 0.65
41 10 0.08
ACGTcount: A:0.24, C:0.23, G:0.27, T:0.25
Consensus pattern (39 bp):
CCGGGCTAAGTCCCGAAGGCATTTGTGCGAGTTACTAAA
Found at i:27821876 original size:79 final size:79
Alignment explanation
Indices: 27821723--27821887 Score: 201
Period size: 79 Copynumber: 2.1 Consensus size: 79
27821713 GAACTAAGAT
* **
27821723 CCGAAGGCATTTGTGCGAGTTACTAATTCCGGCCTAAGCCCGAAGGCATTGGTGCGAGTCACTAA
1 CCGAAGGCATTTGTGCGAGTTACTAATACCGGCCTAAGCCCGAAGGCATTGGAACGAGTCACTAA
*
27821788 ATCCGGGTTAAGTC
66 ATCCGGGTTAAATC
* * *
27821802 CCGAAGGCATTTGTGCGAGTTACT-ATAACCGGGCTATGTCCCGAAGGCATTTGAACGAGT-AGC
1 CCGAAGGCATTTGTGCGAGTTACTAAT-ACCGGCCTAAG-CCCGAAGGCATTGGAACGAGTCA-C
* *
27821865 TATATCC-GGTTAAATT
63 TAAATCCGGGTTAAATC
27821881 CCGAAGG
1 CCGAAGG
27821888 TACGTGATTC
Statistics
Matches: 74, Mismatches: 9, Indels: 6
0.83 0.10 0.07
Matches are distributed among these distances:
78 2 0.03
79 47 0.64
80 25 0.34
ACGTcount: A:0.25, C:0.22, G:0.27, T:0.25
Consensus pattern (79 bp):
CCGAAGGCATTTGTGCGAGTTACTAATACCGGCCTAAGCCCGAAGGCATTGGAACGAGTCACTAA
ATCCGGGTTAAATC
Found at i:27826010 original size:28 final size:28
Alignment explanation
Indices: 27825978--27826033 Score: 94
Period size: 28 Copynumber: 2.0 Consensus size: 28
27825968 AACCTTTTCG
*
27825978 ATGTCGGCCTCTACGTAGTCCACCCAGT
1 ATGTCGGCCTCTACGTAATCCACCCAGT
*
27826006 ATGTCGGCTTCTACGTAATCCACCCAGT
1 ATGTCGGCCTCTACGTAATCCACCCAGT
27826034 TGACAAATGA
Statistics
Matches: 26, Mismatches: 2, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
28 26 1.00
ACGTcount: A:0.20, C:0.34, G:0.20, T:0.27
Consensus pattern (28 bp):
ATGTCGGCCTCTACGTAATCCACCCAGT
Found at i:27830032 original size:46 final size:48
Alignment explanation
Indices: 27829928--27830047 Score: 145
Period size: 48 Copynumber: 2.5 Consensus size: 48
27829918 TGTCTTCGAC
** * *
27829928 ATGGACTTACATGAATTATTCCTGTCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
** * *
27829976 ATGGGTTTACATGGCTCATTCCTGTCTCCAAAGCCATATA-A-CTGAT
1 ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
*
27830022 ATGGACTTACATGGCTCATTTCTGTC
1 ATGGACTTACATGGCTCATTCCTGTC
27830048 CTGTCCTGGC
Statistics
Matches: 61, Mismatches: 11, Indels: 2
0.82 0.15 0.03
Matches are distributed among these distances:
46 26 0.43
47 1 0.02
48 34 0.56
ACGTcount: A:0.28, C:0.22, G:0.15, T:0.36
Consensus pattern (48 bp):
ATGGACTTACATGGCTCATTCCTGTCTCCAAAGCCATATATATATAAT
Found at i:27834281 original size:48 final size:46
Alignment explanation
Indices: 27834212--27834325 Score: 120
Period size: 48 Copynumber: 2.4 Consensus size: 46
27834202 TGTCTTCGAC
** * * *
27834212 ATGGACTTACATGAATTATTCCTATCTCCAATGCCATATATATATAAT
1 ATGGACTTACATGGCTCATTCCTACCTCCAAAGCCATATA-A-ATAAT
* * * * *
27834260 ATGGGCTTACATGGCTCATTCCTGCCTCTAAAGCCATATAACTGAT
1 ATGGACTTACATGGCTCATTCCTACCTCCAAAGCCATATAAATAAT
27834306 ATGGACTTACATGGCTCATT
1 ATGGACTTACATGGCTCATT
27834326 TCTGTCCTGT
Statistics
Matches: 55, Mismatches: 11, Indels: 2
0.81 0.16 0.03
Matches are distributed among these distances:
46 22 0.40
47 1 0.02
48 32 0.58
ACGTcount: A:0.30, C:0.22, G:0.14, T:0.34
Consensus pattern (46 bp):
ATGGACTTACATGGCTCATTCCTACCTCCAAAGCCATATAAATAAT
Found at i:27842774 original size:46 final size:47
Alignment explanation
Indices: 27842626--27842849 Score: 158
Period size: 46 Copynumber: 4.7 Consensus size: 47
27842616 ACTTTATGAG
* * * * *
27842626 AGCCAGTATAAGACCATGTCTGGGACATGGCGTCAG-TATTGAGACGA-G
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTA-TGAGATGATA
* *
27842674 AGCTAGTGTAAGACATGTCTGGGACATGCATCGGCCTCA--AGACG-TA
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGG-CT-ATGAGATGATA
* *
27842720 AGCCAGTGTAAGACATGTCTAGGAAATGCATCGGCTATGAGATGAT-
1 AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTATGAGATGATA
** * * *
27842766 AGTTAGTGTAAGACCGTGTCTGGGACATGGCATCGACT-TGAGAT-ATG
1 AGCCAGTGTAAGA-CATGTCTGGGACAT-GCATCGGCTATGAGATGATA
* **
27842813 AGCCAGTGTAAGACTATGTTTGTAACATGCCATCGGC
1 AGCCAGTGTAAGAC-ATGTCTGGGACATG-CATCGGC
27842850 ATCTTACCCA
Statistics
Matches: 142, Mismatches: 22, Indels: 25
0.75 0.12 0.13
Matches are distributed among these distances:
44 1 0.01
45 2 0.01
46 60 0.42
47 58 0.41
48 20 0.14
49 1 0.01
ACGTcount: A:0.29, C:0.18, G:0.29, T:0.24
Consensus pattern (47 bp):
AGCCAGTGTAAGACATGTCTGGGACATGCATCGGCTATGAGATGATA
Found at i:27846937 original size:41 final size:41
Alignment explanation
Indices: 27846887--27846964 Score: 120
Period size: 41 Copynumber: 1.9 Consensus size: 41
27846877 CTGACACACT
* **
27846887 CCCGCGTCTATGGCCCGTGTCCTTCACTTGGCCATGACATG
1 CCCGCGTCTATGGCCCATGTCCTTCACACGGCCATGACATG
*
27846928 CCCGTGTCTATGGCCCATGTCCTTCACACGGCCATGA
1 CCCGCGTCTATGGCCCATGTCCTTCACACGGCCATGA
27846965 TACTCCTGTG
Statistics
Matches: 33, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
41 33 1.00
ACGTcount: A:0.14, C:0.37, G:0.23, T:0.26
Consensus pattern (41 bp):
CCCGCGTCTATGGCCCATGTCCTTCACACGGCCATGACATG
Found at i:27848634 original size:30 final size:30
Alignment explanation
Indices: 27848573--27848634 Score: 72
Period size: 30 Copynumber: 2.1 Consensus size: 30
27848563 TAAGATTCAT
* * *
27848573 ACTTTGATAAAATGACCGTTTTGCCTCTAG
1 ACTTTCATAAAATGACCATTTTCCCTCTAG
*
27848603 ACTTTCATAAAATGTCCATTTTACCCT-TAG
1 ACTTTCATAAAATGACCATTTT-CCCTCTAG
27848633 AC
1 AC
27848635 CCAAAAATTG
Statistics
Matches: 27, Mismatches: 4, Indels: 2
0.82 0.12 0.06
Matches are distributed among these distances:
30 24 0.89
31 3 0.11
ACGTcount: A:0.29, C:0.23, G:0.11, T:0.37
Consensus pattern (30 bp):
ACTTTCATAAAATGACCATTTTCCCTCTAG
Found at i:27851317 original size:40 final size:40
Alignment explanation
Indices: 27851273--27851413 Score: 162
Period size: 40 Copynumber: 3.5 Consensus size: 40
27851263 ATTTGATGTG
*
27851273 TGTATCCGGGCTTAAAGACCCGCAGACTATATG-TGGGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGACTATATGCT-GGAAT
*
27851313 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGCTGGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGACTATATGCTGGAAT
* * * *
27851353 TGTATCAGGGTTTAAAGGCCCGCAGGCT-TCGTGCTGGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGACTAT-ATGCTGGAAT
* * *
27851393 GGAATCTGGG-TTAAAGACCCG
1 TGTATCCGGGTTTAAAGACCCG
27851414 TAGGCTCGTG
Statistics
Matches: 90, Mismatches: 9, Indels: 5
0.87 0.09 0.05
Matches are distributed among these distances:
39 11 0.12
40 78 0.87
41 1 0.01
ACGTcount: A:0.25, C:0.20, G:0.30, T:0.26
Consensus pattern (40 bp):
TGTATCCGGGTTTAAAGACCCGCAGACTATATGCTGGAAT
Found at i:27859044 original size:40 final size:40
Alignment explanation
Indices: 27859000--27859146 Score: 190
Period size: 40 Copynumber: 3.7 Consensus size: 40
27858990 ATTTGATGTG
* *
27859000 TGTATCCGGGCTTAAAGACCCGCAGACTATATGCTGGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGCTGGAAT
*
27859040 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGCTAGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGGCTATATGCTGGAAT
* * *
27859080 TGTATCCAGGTTTAAAGGCCCGCAGGCT-TCGTGCTGGAAT
1 TGTATCCGGGTTTAAAGACCCGCAGGCTAT-ATGCTGGAAT
* * *
27859120 GGAATCCGGG-TTAAAGACCCGTAGGCT
1 TGTATCCGGGTTTAAAGACCCGCAGGCT
27859147 CGTGTTAGAA
Statistics
Matches: 94, Mismatches: 12, Indels: 3
0.86 0.11 0.03
Matches are distributed among these distances:
39 16 0.17
40 78 0.83
ACGTcount: A:0.25, C:0.22, G:0.28, T:0.25
Consensus pattern (40 bp):
TGTATCCGGGTTTAAAGACCCGCAGGCTATATGCTGGAAT
Found at i:27862718 original size:27 final size:27
Alignment explanation
Indices: 27862688--27862755 Score: 91
Period size: 27 Copynumber: 2.5 Consensus size: 27
27862678 AATGCTCTTG
*
27862688 TAGGGTAAAATGACCGTAATACCCCTA
1 TAGGGTAAAATGACCATAATACCCCTA
* * *
27862715 TAGGGTAAAATGATCATAATACCCTTC
1 TAGGGTAAAATGACCATAATACCCCTA
*
27862742 TATGGTAAAATGAC
1 TAGGGTAAAATGAC
27862756 GATTATGCCC
Statistics
Matches: 35, Mismatches: 6, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 35 1.00
ACGTcount: A:0.38, C:0.18, G:0.18, T:0.26
Consensus pattern (27 bp):
TAGGGTAAAATGACCATAATACCCCTA
Found at i:27882665 original size:15 final size:15
Alignment explanation
Indices: 27882645--27882673 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
27882635 ATGCTTGACA
27882645 CACCGTGTTATCAAT
1 CACCGTGTTATCAAT
27882660 CACCGTGTTATCAA
1 CACCGTGTTATCAA
27882674 GCAACAATAC
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.28, C:0.28, G:0.14, T:0.31
Consensus pattern (15 bp):
CACCGTGTTATCAAT
Found at i:27900569 original size:50 final size:50
Alignment explanation
Indices: 27900440--27900635 Score: 191
Period size: 50 Copynumber: 3.9 Consensus size: 50
27900430 CGATAATAAC
* * * * *
27900440 ATGCCAAAGCCATGTCCCAGACATGGTCTTACATGGGA--TGT-TTTTTG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * * **
27900487 TACTGCCAATGCCATATCCCAGATATAGTCTTACATGGGAGTTCTCATATCG
1 -A-TGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * ** *
27900539 ATGCCCATGCCATGTCCTAGACATGGTCTTACGGGGGACCTCTCATCTCG
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
* * *
27900589 GTGCCAACGCCATGTCCTAGACATGGTCTTACATGGGACCTCTCATA
1 ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATA
27900636 ATCTCAATGA
Statistics
Matches: 120, Mismatches: 24, Indels: 6
0.80 0.16 0.04
Matches are distributed among these distances:
48 1 0.01
49 33 0.28
50 80 0.67
51 3 0.03
52 3 0.03
ACGTcount: A:0.23, C:0.27, G:0.21, T:0.29
Consensus pattern (50 bp):
ATGCCAATGCCATGTCCCAGACATGGTCTTACATGGGACCTCTCATATCG
Found at i:27901059 original size:30 final size:30
Alignment explanation
Indices: 27901025--27901082 Score: 80
Period size: 30 Copynumber: 1.9 Consensus size: 30
27901015 CATTGAATCG
27901025 AACTTTGGAAAAATTACAATTTTGCCCCTA
1 AACTTTGGAAAAATTACAATTTTGCCCCTA
* * * *
27901055 AACTTTTGCATAATTACACTTTTGCCCC
1 AACTTTGGAAAAATTACAATTTTGCCCC
27901083 AAAGCTCGAA
Statistics
Matches: 24, Mismatches: 4, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
30 24 1.00
ACGTcount: A:0.31, C:0.24, G:0.09, T:0.36
Consensus pattern (30 bp):
AACTTTGGAAAAATTACAATTTTGCCCCTA
Found at i:27916770 original size:3 final size:3
Alignment explanation
Indices: 27916762--27916799 Score: 58
Period size: 3 Copynumber: 12.7 Consensus size: 3
27916752 GTAACTATAG
* *
27916762 TGA TGA TGA TAA TGA TGA TGA TGA TGA TTA TGA TGA TG
1 TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TGA TG
27916800 TTTTTTGAAT
Statistics
Matches: 31, Mismatches: 4, Indels: 0
0.89 0.11 0.00
Matches are distributed among these distances:
3 31 1.00
ACGTcount: A:0.34, C:0.00, G:0.29, T:0.37
Consensus pattern (3 bp):
TGA
Found at i:27917088 original size:15 final size:16
Alignment explanation
Indices: 27917068--27917097 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27917058 AGGCAAAGTA
27917068 AAATA-TTTAAAAAAT
1 AAATATTTTAAAAAAT
27917083 AAATATTTTAAAAAA
1 AAATATTTTAAAAAA
27917098 GAGGTACGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 1
0.93 0.00 0.07
Matches are distributed among these distances:
15 5 0.36
16 9 0.64
ACGTcount: A:0.67, C:0.00, G:0.00, T:0.33
Consensus pattern (16 bp):
AAATATTTTAAAAAAT
Found at i:27927971 original size:56 final size:50
Alignment explanation
Indices: 27927766--27927988 Score: 223
Period size: 50 Copynumber: 4.3 Consensus size: 50
27927756 CAATGCCACA
* ** * * * *
27927766 TCCCAGATATGGTCTTACATGGGAGTTCTCATAT-AGGTGCCCATGCGATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCA-GTGCCAACGCCATG
* ** * * *
27927816 TCCCAGATATGGTCTTACGGGGGACCTCACATATCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATG
27927866 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATG
** * *
27927916 TCTGAGACATGGTCTTACATGGGACCTCTCATTATCTCAATGATGGCAATGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTC---ATCTC-A-G-TGCCAACGCCATG
27927972 TCCCAGACATGGTCTTA
1 TCCCAGACATGGTCTTA
27927989 TATGAGATCT
Statistics
Matches: 145, Mismatches: 21, Indels: 8
0.83 0.12 0.05
Matches are distributed among these distances:
50 112 0.77
53 5 0.03
54 1 0.01
55 1 0.01
56 26 0.18
ACGTcount: A:0.23, C:0.27, G:0.23, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATCTCAGTGCCAACGCCATG
Found at i:27934906 original size:49 final size:50
Alignment explanation
Indices: 27934756--27934937 Score: 215
Period size: 50 Copynumber: 3.7 Consensus size: 50
27934746 CAATGACACA
* * ** * * *
27934756 TCCCAGATATGATCTTACATGGGAGTTCTCATATAGGTGTCC-ATGCGATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTG-CCAACGCCATG
* * * *
27934806 TCCCAGATATGGTCTTACAGGGGGCCTCACATATCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
*
27934856 TCCCAGACATGGTCTTA-ATGGGACCTCTCATCTCGGTGCCAACGCCATG
1 TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
* *
27934905 TCCCAGGCATGGTTTTACATGGGACCTCTCATA
1 TCCCAGACATGGTCTTACATGGGACCTCTCATA
27934938 GTCTCAATAA
Statistics
Matches: 113, Mismatches: 17, Indels: 4
0.84 0.13 0.03
Matches are distributed among these distances:
49 45 0.40
50 68 0.60
ACGTcount: A:0.22, C:0.27, G:0.24, T:0.27
Consensus pattern (50 bp):
TCCCAGACATGGTCTTACATGGGACCTCTCATATCGGTGCCAACGCCATG
Found at i:27936495 original size:37 final size:36
Alignment explanation
Indices: 27936446--27936515 Score: 106
Period size: 37 Copynumber: 1.9 Consensus size: 36
27936436 GTTTAGCATC
*
27936446 TTTTCCTATTGTGTTTGGA-CGAATATACCTGAACTA
1 TTTTCCTATTGTGTTT-GACCAAATATACCTGAACTA
27936482 TTTTCCCTATTGTGTTTGACCAAATATACCTGAA
1 TTTT-CCTATTGTGTTTGACCAAATATACCTGAA
27936516 TTACTCCAAC
Statistics
Matches: 31, Mismatches: 1, Indels: 3
0.89 0.03 0.09
Matches are distributed among these distances:
36 6 0.19
37 25 0.81
ACGTcount: A:0.26, C:0.19, G:0.14, T:0.41
Consensus pattern (36 bp):
TTTTCCTATTGTGTTTGACCAAATATACCTGAACTA
Found at i:27938037 original size:34 final size:34
Alignment explanation
Indices: 27937982--27938046 Score: 78
Period size: 34 Copynumber: 1.9 Consensus size: 34
27937972 ATTTGCCACC
*
27937982 GTTACTGTAATGGGGTAAGGCCCACACTGATACT
1 GTTACTGTAATGGGCTAAGGCCCACACTGATACT
* * *
27938016 GTTACTGTTAA-GGGCTCAGGCCTAGACTGAT
1 GTTACTG-TAATGGGCTAAGGCCCACACTGAT
27938047 TCTATTTCTT
Statistics
Matches: 26, Mismatches: 4, Indels: 2
0.81 0.12 0.06
Matches are distributed among these distances:
34 23 0.88
35 3 0.12
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.28
Consensus pattern (34 bp):
GTTACTGTAATGGGCTAAGGCCCACACTGATACT
Found at i:27944856 original size:16 final size:16
Alignment explanation
Indices: 27944835--27944865 Score: 53
Period size: 16 Copynumber: 1.9 Consensus size: 16
27944825 TTTACTATTA
*
27944835 TGTCTTTTGTATTTTT
1 TGTCTTTTATATTTTT
27944851 TGTCTTTTATATTTT
1 TGTCTTTTATATTTT
27944866 GCATGCATAG
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
16 14 1.00
ACGTcount: A:0.10, C:0.06, G:0.10, T:0.74
Consensus pattern (16 bp):
TGTCTTTTATATTTTT
Found at i:27946963 original size:24 final size:24
Alignment explanation
Indices: 27946936--27946981 Score: 65
Period size: 24 Copynumber: 1.9 Consensus size: 24
27946926 CTAATTAAAT
* *
27946936 TTTATAAATAATTAATATTTATTG
1 TTTAAAAATAATTAAAATTTATTG
*
27946960 TTTAAAAATATTTAAAATTTAT
1 TTTAAAAATAATTAAAATTTAT
27946982 ATTTCATATA
Statistics
Matches: 19, Mismatches: 3, Indels: 0
0.86 0.14 0.00
Matches are distributed among these distances:
24 19 1.00
ACGTcount: A:0.46, C:0.00, G:0.02, T:0.52
Consensus pattern (24 bp):
TTTAAAAATAATTAAAATTTATTG
Found at i:27947192 original size:13 final size:13
Alignment explanation
Indices: 27947176--27947226 Score: 66
Period size: 13 Copynumber: 3.9 Consensus size: 13
27947166 TTTAAACCAA
27947176 ACTTTTCAAAAGC
1 ACTTTTCAAAAGC
*
27947189 ACTTTCCAAAAGC
1 ACTTTTCAAAAGC
* * *
27947202 ACTTCTCCACAGC
1 ACTTTTCAAAAGC
27947215 ACTTTTCAAAAG
1 ACTTTTCAAAAG
27947227 TAATGAAGAA
Statistics
Matches: 30, Mismatches: 8, Indels: 0
0.79 0.21 0.00
Matches are distributed among these distances:
13 30 1.00
ACGTcount: A:0.35, C:0.29, G:0.08, T:0.27
Consensus pattern (13 bp):
ACTTTTCAAAAGC
Found at i:27947371 original size:23 final size:23
Alignment explanation
Indices: 27947342--27947463 Score: 163
Period size: 23 Copynumber: 5.3 Consensus size: 23
27947332 ATAAGTGCCA
27947342 CACTGATATGTAGCCGAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
27947365 CACTGATACGTAGCCGTAGCTAG
1 CACTGATATGTAGCCGAAGCTAC
* *
27947388 CACTGAAATGTAGCCAAAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
*
27947411 CACTGATATGTAGCCGTAGCTAC
1 CACTGATATGTAGCCGAAGCTAC
* * *
27947434 CACTGAAATGTACCCGAAGTTAC
1 CACTGATATGTAGCCGAAGCTAC
27947457 CACTGAT
1 CACTGAT
27947464 CAATAACACT
Statistics
Matches: 83, Mismatches: 16, Indels: 0
0.84 0.16 0.00
Matches are distributed among these distances:
23 83 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (23 bp):
CACTGATATGTAGCCGAAGCTAC
Found at i:27947409 original size:46 final size:46
Alignment explanation
Indices: 27947342--27947463 Score: 190
Period size: 46 Copynumber: 2.7 Consensus size: 46
27947332 ATAAGTGCCA
* *
27947342 CACTGATATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTAG
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTAC
* *
27947388 CACTGAAATGTAGCCAAAGCTACCACTGATATGTAGCCGTAGCTAC
1 CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTAC
* *
27947434 CACTGAAATGTACCCGAAGTTACCACTGAT
1 CACTGAAATGTAGCCGAAGCTACCACTGAT
27947464 CAATAACACT
Statistics
Matches: 69, Mismatches: 7, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
46 69 1.00
ACGTcount: A:0.31, C:0.26, G:0.20, T:0.22
Consensus pattern (46 bp):
CACTGAAATGTAGCCGAAGCTACCACTGATACGTAGCCGTAGCTAC
Found at i:27953202 original size:23 final size:21
Alignment explanation
Indices: 27953142--27953202 Score: 70
Period size: 23 Copynumber: 2.8 Consensus size: 21
27953132 AGTCTTTTTA
27953142 TTGATA-TATGAATATTATGT
1 TTGATATTATGAATATTATGT
*
27953162 TTGTTAATATATGAATATTATGT
1 TTGAT-AT-TATGAATATTATGT
27953185 TTGGATATTATGACATAT
1 TT-GATATTATGA-ATAT
27953203 AAACTAATGA
Statistics
Matches: 34, Mismatches: 2, Indels: 7
0.79 0.05 0.16
Matches are distributed among these distances:
20 4 0.12
21 1 0.03
22 5 0.15
23 22 0.65
24 2 0.06
ACGTcount: A:0.34, C:0.02, G:0.15, T:0.49
Consensus pattern (21 bp):
TTGATATTATGAATATTATGT
Found at i:27953432 original size:21 final size:21
Alignment explanation
Indices: 27953387--27953433 Score: 62
Period size: 21 Copynumber: 2.3 Consensus size: 21
27953377 AAATAATAAA
*
27953387 ATAG-ATTATATATTATTTTT
1 ATAGTATTATATATTATATTT
27953407 ATAGTATTATATATTATGATTT
1 ATAGTATTATATATTAT-ATTT
27953429 -TAGTA
1 ATAGTA
27953434 AATTCATATA
Statistics
Matches: 24, Mismatches: 1, Indels: 3
0.86 0.04 0.11
Matches are distributed among these distances:
20 4 0.17
21 17 0.71
22 3 0.12
ACGTcount: A:0.36, C:0.00, G:0.09, T:0.55
Consensus pattern (21 bp):
ATAGTATTATATATTATATTT
Found at i:27953744 original size:45 final size:44
Alignment explanation
Indices: 27953655--27953747 Score: 143
Period size: 44 Copynumber: 2.1 Consensus size: 44
27953645 ATTACAACAT
*
27953655 CATTCCATTCAACCAAACACAAGAATACTATTCCAGTTCTATTC
1 CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
*
27953699 CATTCCATTCAACCAAACA-ATTGAATTACTATTACAGTTCTATTC
1 CATTCCATTCAACCAAACACA-AGAA-TACTATTACAGTTCTATTC
27953744 CATT
1 CATT
27953748 ACAGCTCTAT
Statistics
Matches: 45, Mismatches: 2, Indels: 3
0.90 0.04 0.06
Matches are distributed among these distances:
43 1 0.02
44 22 0.49
45 22 0.49
ACGTcount: A:0.35, C:0.27, G:0.04, T:0.33
Consensus pattern (44 bp):
CATTCCATTCAACCAAACACAAGAATACTATTACAGTTCTATTC
Found at i:27953750 original size:16 final size:16
Alignment explanation
Indices: 27953729--27953768 Score: 62
Period size: 16 Copynumber: 2.5 Consensus size: 16
27953719 TTGAATTACT
* *
27953729 ATTACAGTTCTATTCC
1 ATTACAGCTCTATTCA
27953745 ATTACAGCTCTATTCA
1 ATTACAGCTCTATTCA
27953761 ATTACAGC
1 ATTACAGC
27953769 GAACCAAACG
Statistics
Matches: 22, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
16 22 1.00
ACGTcount: A:0.30, C:0.25, G:0.07, T:0.38
Consensus pattern (16 bp):
ATTACAGCTCTATTCA
Found at i:27956516 original size:17 final size:19
Alignment explanation
Indices: 27956489--27956523 Score: 56
Period size: 17 Copynumber: 1.9 Consensus size: 19
27956479 CCCTCATCCT
27956489 CTAAGGGGAAATA-GAAAG
1 CTAAGGGGAAATATGAAAG
27956507 CTAA-GGGAAATATGAAA
1 CTAAGGGGAAATATGAAA
27956524 CCGACTATGT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
17 8 0.50
18 8 0.50
ACGTcount: A:0.51, C:0.06, G:0.29, T:0.14
Consensus pattern (19 bp):
CTAAGGGGAAATATGAAAG
Found at i:27958467 original size:42 final size:42
Alignment explanation
Indices: 27958403--27958484 Score: 121
Period size: 42 Copynumber: 2.0 Consensus size: 42
27958393 TTTATAGCTT
* *
27958403 TTTTCCAACAACCCATGTTTATCTTCTCCTATTTTTAAATTCA
1 TTTTCCAACAACCCAAGATTATCTTCTCCT-TTTTTAAATTCA
*
27958446 TTTT-CAACAACGCAAGATTATCTTCTCCTTTTTTAAATT
1 TTTTCCAACAACCCAAGATTATCTTCTCCTTTTTTAAATT
27958485 TTTTTCTAGG
Statistics
Matches: 36, Mismatches: 3, Indels: 2
0.88 0.07 0.05
Matches are distributed among these distances:
41 10 0.28
42 22 0.61
43 4 0.11
ACGTcount: A:0.27, C:0.23, G:0.04, T:0.46
Consensus pattern (42 bp):
TTTTCCAACAACCCAAGATTATCTTCTCCTTTTTTAAATTCA
Found at i:27978249 original size:27 final size:27
Alignment explanation
Indices: 27978219--27978271 Score: 70
Period size: 27 Copynumber: 2.0 Consensus size: 27
27978209 TTTTTCAAAA
*
27978219 ATCAAATGATATAACTTTTGACTAATG
1 ATCAAAAGATATAACTTTTGACTAATG
* * *
27978246 ATCAAAAGATTTATCTTTTGATTAAT
1 ATCAAAAGATATAACTTTTGACTAAT
27978272 TACACCCATT
Statistics
Matches: 22, Mismatches: 4, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
27 22 1.00
ACGTcount: A:0.40, C:0.09, G:0.09, T:0.42
Consensus pattern (27 bp):
ATCAAAAGATATAACTTTTGACTAATG
Found at i:27991790 original size:394 final size:396
Alignment explanation
Indices: 27991018--27991792 Score: 1464
Period size: 396 Copynumber: 2.0 Consensus size: 396
27991008 TATGCTAAGG
27991018 TACCATTCGTCATTTGGTTACTGTTTTTGCCGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAT
1 TACCATTCGTCATTTGGTTACTGTTTTTGCCGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAT
27991083 TTGGATAGGAAAGAAAATAAAATAATTAAAAGTATTTATATATATCATTTATTTTAGAACAAAAT
66 TTGGATAGGAAAGAAAATAAAATAATTAAAAGTATTTATATATATCATTTATTTTAGAACAAAAT
*
27991148 AATTTGATTTTTCTTTTAATAGAACAGTTATACTAGACATTTCGTTACATTTTAGTCATATATTT
131 AATTTGATTTTTCTTTTAATAGAACAGTTATACTAGAAATTTCGTTACATTTTAGTCATATATTT
27991213 TCAAACAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTTAAAAAATCAAAAGC
196 TCAAACAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTTAAAAAATCAAAAGC
27991278 TCAAAAAGAAGACACAAGGTTGAACCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
261 TCAAAAAGAAGACACAAGGTTGAACCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
*
27991343 GAACACAGACCATAAAATGGACATGGAGAATACCAAAATACAAGAAACAAAAAGCAAAAATACAT
326 GAACACAGACCATAAAATGGAAATGGAGAATACCAAAATACAAGAAACAAAAAGCAAAAATACAT
27991408 GGAGAA
391 GGAGAA
* *
27991414 TACCATTTGTCATTTGGTTACTGTTTTTGCTGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAT
1 TACCATTCGTCATTTGGTTACTGTTTTTGCCGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAT
* *
27991479 TTGGATAGGAAAGGAAATAAAATAATTAAAAGTATTTATATATATCATTTATTTTAGAATAAAAT
66 TTGGATAGGAAAGAAAATAAAATAATTAAAAGTATTTATATATATCATTTATTTTAGAACAAAAT
27991544 AATTTGA-TTTTCTTTTAATAGAACAGTTATACTAGAAATTTCGTTACATTTTAGTCATATATTT
131 AATTTGATTTTTCTTTTAATAGAACAGTTATACTAGAAATTTCGTTACATTTTAGTCATATATTT
*
27991608 TCAATCAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTT-AAAAATCAAAAGC
196 TCAAACAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTTAAAAAATCAAAAGC
*
27991672 TCAAAAAGAAGACACAAGGTTGATCCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
261 TCAAAAAGAAGACACAAGGTTGAACCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
27991737 GAACACAGACCATAAAATGGAAATGGAGAATACCAAAATACAAGAAACAAAAAGCA
326 GAACACAGACCATAAAATGGAAATGGAGAATACCAAAATACAAGAAACAAAAAGCA
27991793 TATTTGCGGA
Statistics
Matches: 371, Mismatches: 8, Indels: 2
0.97 0.02 0.01
Matches are distributed among these distances:
394 132 0.36
395 106 0.29
396 133 0.36
ACGTcount: A:0.38, C:0.16, G:0.14, T:0.31
Consensus pattern (396 bp):
TACCATTCGTCATTTGGTTACTGTTTTTGCCGCCAGTTTTTTGCTTCCACAAGCAAAAAGTACAT
TTGGATAGGAAAGAAAATAAAATAATTAAAAGTATTTATATATATCATTTATTTTAGAACAAAAT
AATTTGATTTTTCTTTTAATAGAACAGTTATACTAGAAATTTCGTTACATTTTAGTCATATATTT
TCAAACAATTATGACTTTGCTTTCTCCCTTCCCACTTTCCAGCAGCCTTTTAAAAAATCAAAAGC
TCAAAAAGAAGACACAAGGTTGAACCTTGGAGACAAAATTGTTGGGAGGGACAATCGCGAATCCT
GAACACAGACCATAAAATGGAAATGGAGAATACCAAAATACAAGAAACAAAAAGCAAAAATACAT
GGAGAA
Found at i:27995927 original size:15 final size:15
Alignment explanation
Indices: 27995907--27995936 Score: 51
Period size: 15 Copynumber: 2.0 Consensus size: 15
27995897 TTTGTAAATG
*
27995907 TTCTTTACCTGAGGA
1 TTCTTTACCTCAGGA
27995922 TTCTTTACCTCAGGA
1 TTCTTTACCTCAGGA
27995937 ACAGTTATGC
Statistics
Matches: 14, Mismatches: 1, Indels: 0
0.93 0.07 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.20, C:0.23, G:0.17, T:0.40
Consensus pattern (15 bp):
TTCTTTACCTCAGGA
Found at i:28007163 original size:24 final size:25
Alignment explanation
Indices: 28007100--28007163 Score: 69
Period size: 25 Copynumber: 2.6 Consensus size: 25
28007090 TTACTGATAC
28007100 TCAGCTCGTATGAGCTGACCATTAT
1 TCAGCTCGTATGAGCTGACCATTAT
* * * *
28007125 TCAGCTCGGAGGAGCTTACCGTT-T
1 TCAGCTCGTATGAGCTGACCATTAT
28007149 ATC-GCTCGTATGAGC
1 -TCAGCTCGTATGAGC
28007164 AAACATGTAC
Statistics
Matches: 32, Mismatches: 6, Indels: 3
0.78 0.15 0.07
Matches are distributed among these distances:
24 11 0.34
25 21 0.66
ACGTcount: A:0.20, C:0.25, G:0.25, T:0.30
Consensus pattern (25 bp):
TCAGCTCGTATGAGCTGACCATTAT
Found at i:28010338 original size:45 final size:45
Alignment explanation
Indices: 28010274--28010416 Score: 137
Period size: 45 Copynumber: 3.2 Consensus size: 45
28010264 TCTTACAAAT
** *
28010274 ACCATAGCTGAAAGATGTTATAGTGTCACTG-CAAAAATGAGTAAG
1 ACCATAGCTGAAAGATGTTATAGCATCA-TGAAAAAAATGAGTAAG
* *
28010319 ACCATAGTTGAAAGATGTTATGGCATCATGAAAAAAATGAGTAAG
1 ACCATAGCTGAAAGATGTTATAGCATCATGAAAAAAATGAGTAAG
* * * * ** * *
28010364 ACCATAGC-CAACAGACGCTATGGCATCATGGTAGAAATAAGTAAG
1 ACCATAGCTGAA-AGATGTTATAGCATCATGAAAAAAATGAGTAAG
28010409 ACCATAGC
1 ACCATAGC
28010417 CAAAAGACAT
Statistics
Matches: 83, Mismatches: 13, Indels: 4
0.83 0.13 0.04
Matches are distributed among these distances:
44 4 0.05
45 79 0.95
ACGTcount: A:0.41, C:0.15, G:0.22, T:0.22
Consensus pattern (45 bp):
ACCATAGCTGAAAGATGTTATAGCATCATGAAAAAAATGAGTAAG
Found at i:28010417 original size:45 final size:45
Alignment explanation
Indices: 28010337--28010438 Score: 141
Period size: 45 Copynumber: 2.3 Consensus size: 45
28010327 TGAAAGATGT
* * *
28010337 TATGGCATCATGAAAAAAATGAGTAAGACCATAGCCAACAGACGC
1 TATGGCATCATGAAAAAAATAAGTAAGACCATAGCCAAAAGACAC
** * *
28010382 TATGGCATCATGGTAGAAATAAGTAAGACCATAGCCAAAAGACAT
1 TATGGCATCATGAAAAAAATAAGTAAGACCATAGCCAAAAGACAC
28010427 TATGGCATCATG
1 TATGGCATCATG
28010439 TGAAACACGC
Statistics
Matches: 50, Mismatches: 7, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
45 50 1.00
ACGTcount: A:0.42, C:0.18, G:0.21, T:0.20
Consensus pattern (45 bp):
TATGGCATCATGAAAAAAATAAGTAAGACCATAGCCAAAAGACAC
Found at i:28011635 original size:46 final size:46
Alignment explanation
Indices: 28011559--28011651 Score: 123
Period size: 46 Copynumber: 2.0 Consensus size: 46
28011549 CTCTATATAA
* * *
28011559 AGTTTGTAAATTTCCATCAAAATAAATGTCTTAAAGATTTATTACC
1 AGTTTGCAAATGTCCATCAAAATAAATGTCTTAAAGATTTATAACC
* * * *
28011605 AGTTTGCAAATGTCCGTCAGAATCAATGTCTTAGAGATTTATAACC
1 AGTTTGCAAATGTCCATCAAAATAAATGTCTTAAAGATTTATAACC
28011651 A
1 A
28011652 CTTAATGCGA
Statistics
Matches: 40, Mismatches: 7, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
46 40 1.00
ACGTcount: A:0.37, C:0.15, G:0.13, T:0.35
Consensus pattern (46 bp):
AGTTTGCAAATGTCCATCAAAATAAATGTCTTAAAGATTTATAACC
Found at i:28030748 original size:13 final size:13
Alignment explanation
Indices: 28030713--28030749 Score: 56
Period size: 13 Copynumber: 2.8 Consensus size: 13
28030703 ACTTTGTATA
28030713 ATTTTCTCTTTAG
1 ATTTTCTCTTTAG
**
28030726 ATTTAGTCTTTAG
1 ATTTTCTCTTTAG
28030739 ATTTTCTCTTT
1 ATTTTCTCTTT
28030750 TCTTAGGTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
13 20 1.00
ACGTcount: A:0.16, C:0.14, G:0.08, T:0.62
Consensus pattern (13 bp):
ATTTTCTCTTTAG
Found at i:28032442 original size:18 final size:19
Alignment explanation
Indices: 28032399--28032444 Score: 58
Period size: 19 Copynumber: 2.5 Consensus size: 19
28032389 ATTAGCGAAT
* *
28032399 GAAGTGCATCTTGGCACAC
1 GAAGTGCATCCTAGCACAC
28032418 GAAGTGCATCCTAGCACA-
1 GAAGTGCATCCTAGCACAC
*
28032436 TAAGTGCAT
1 GAAGTGCAT
28032445 AAACTCATAT
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
18 8 0.33
19 16 0.67
ACGTcount: A:0.30, C:0.24, G:0.24, T:0.22
Consensus pattern (19 bp):
GAAGTGCATCCTAGCACAC
Found at i:28033702 original size:19 final size:19
Alignment explanation
Indices: 28033678--28033715 Score: 67
Period size: 19 Copynumber: 2.0 Consensus size: 19
28033668 ATAAAAATAG
28033678 TGGTATCGATAATTAATTT
1 TGGTATCGATAATTAATTT
*
28033697 TGGTATTGATAATTAATTT
1 TGGTATCGATAATTAATTT
28033716 GTTGTATCAA
Statistics
Matches: 18, Mismatches: 1, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
19 18 1.00
ACGTcount: A:0.32, C:0.03, G:0.16, T:0.50
Consensus pattern (19 bp):
TGGTATCGATAATTAATTT
Found at i:28037460 original size:21 final size:21
Alignment explanation
Indices: 28037434--28037477 Score: 61
Period size: 21 Copynumber: 2.1 Consensus size: 21
28037424 TCCAGCTTCT
* *
28037434 GGCGAGGGTTATGGTTGCTCC
1 GGCGAGGATTATGGTTCCTCC
*
28037455 GGCGAGGATTCTGGTTCCTCC
1 GGCGAGGATTATGGTTCCTCC
28037476 GG
1 GG
28037478 TAGGGGATCT
Statistics
Matches: 20, Mismatches: 3, Indels: 0
0.87 0.13 0.00
Matches are distributed among these distances:
21 20 1.00
ACGTcount: A:0.09, C:0.23, G:0.41, T:0.27
Consensus pattern (21 bp):
GGCGAGGATTATGGTTCCTCC
Found at i:28037759 original size:18 final size:18
Alignment explanation
Indices: 28037733--28037775 Score: 68
Period size: 18 Copynumber: 2.4 Consensus size: 18
28037723 GACTAGAAAA
* *
28037733 AGGAAACATAAAAGGGTT
1 AGGATACATAAAAGGGCT
28037751 AGGATACATAAAAGGGCT
1 AGGATACATAAAAGGGCT
28037769 AGGATAC
1 AGGATAC
28037776 GCACCTGGCA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
18 23 1.00
ACGTcount: A:0.47, C:0.09, G:0.28, T:0.16
Consensus pattern (18 bp):
AGGATACATAAAAGGGCT
Found at i:28037859 original size:30 final size:30
Alignment explanation
Indices: 28037825--28037900 Score: 82
Period size: 30 Copynumber: 2.5 Consensus size: 30
28037815 GTCGGTTGAA
*
28037825 TTGCTGGGTTGGGTGACTGTGTCGGTGCTG
1 TTGCTGGGTTGGGTGACTGTATCGGTGCTG
* * *
28037855 TTGCTGGGTCT-GATGATTGTATTGGTGCTG
1 TTGCTGGGT-TGGGTGACTGTATCGGTGCTG
* *
28037885 ATGATGGGTTGGGTGA
1 TTGCTGGGTTGGGTGA
28037901 TTGTTTGGGC
Statistics
Matches: 37, Mismatches: 7, Indels: 4
0.77 0.15 0.08
Matches are distributed among these distances:
29 1 0.03
30 35 0.95
31 1 0.03
ACGTcount: A:0.09, C:0.09, G:0.43, T:0.38
Consensus pattern (30 bp):
TTGCTGGGTTGGGTGACTGTATCGGTGCTG
Found at i:28039618 original size:11 final size:11
Alignment explanation
Indices: 28039604--28039660 Score: 64
Period size: 11 Copynumber: 5.2 Consensus size: 11
28039594 AATTTTAAAT
28039604 AGGAAATTGAG
1 AGGAAATTGAG
*
28039615 AGGAAACTGAG
1 AGGAAATTGAG
*
28039626 AGGAAATTTAG
1 AGGAAATTGAG
28039637 A-GAATATT-AG
1 AGGAA-ATTGAG
28039647 AGAGAAATTGAG
1 AG-GAAATTGAG
28039659 AG
1 AG
28039661 AAAGGATTTA
Statistics
Matches: 39, Mismatches: 3, Indels: 7
0.80 0.06 0.14
Matches are distributed among these distances:
10 6 0.15
11 26 0.67
12 7 0.18
ACGTcount: A:0.47, C:0.02, G:0.32, T:0.19
Consensus pattern (11 bp):
AGGAAATTGAG
Found at i:28040254 original size:21 final size:21
Alignment explanation
Indices: 28040230--28040282 Score: 88
Period size: 21 Copynumber: 2.5 Consensus size: 21
28040220 CACCATTATT
28040230 TCTAATCTCACTGCTACAGTA
1 TCTAATCTCACTGCTACAGTA
*
28040251 TCTAATCTCACTGCTATAGTA
1 TCTAATCTCACTGCTACAGTA
*
28040272 TCTAATTTCAC
1 TCTAATCTCAC
28040283 CGCCACCGCT
Statistics
Matches: 30, Mismatches: 2, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
21 30 1.00
ACGTcount: A:0.28, C:0.26, G:0.08, T:0.38
Consensus pattern (21 bp):
TCTAATCTCACTGCTACAGTA
Found at i:28040598 original size:6 final size:6
Alignment explanation
Indices: 28040587--28040615 Score: 58
Period size: 6 Copynumber: 4.8 Consensus size: 6
28040577 CAAAGAAGAA
28040587 TAATAG TAATAG TAATAG TAATAG TAATA
1 TAATAG TAATAG TAATAG TAATAG TAATA
28040616 AAATCGAATC
Statistics
Matches: 23, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
6 23 1.00
ACGTcount: A:0.52, C:0.00, G:0.14, T:0.34
Consensus pattern (6 bp):
TAATAG
Found at i:28043205 original size:22 final size:22
Alignment explanation
Indices: 28043180--28043222 Score: 52
Period size: 22 Copynumber: 2.0 Consensus size: 22
28043170 TAATTTCAAG
28043180 TTTAAATT-TGTACTAACTATTC
1 TTTAAATTATGT-CTAACTATTC
**
28043202 TTTATTTTATGTCTAACTATT
1 TTTAAATTATGTCTAACTATT
28043223 GTGATACATA
Statistics
Matches: 18, Mismatches: 2, Indels: 2
0.82 0.09 0.09
Matches are distributed among these distances:
22 15 0.83
23 3 0.17
ACGTcount: A:0.28, C:0.12, G:0.05, T:0.56
Consensus pattern (22 bp):
TTTAAATTATGTCTAACTATTC
Found at i:28049610 original size:20 final size:21
Alignment explanation
Indices: 28049575--28049613 Score: 62
Period size: 20 Copynumber: 1.9 Consensus size: 21
28049565 AAATAGTCAC
*
28049575 TTTTATTTATTTTATATTTTA
1 TTTTAATTATTTTATATTTTA
28049596 TTTTAATTA-TTTATATTT
1 TTTTAATTATTTTATATTT
28049614 AAAATATTAT
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
20 9 0.53
21 8 0.47
ACGTcount: A:0.26, C:0.00, G:0.00, T:0.74
Consensus pattern (21 bp):
TTTTAATTATTTTATATTTTA
Found at i:28049638 original size:15 final size:13
Alignment explanation
Indices: 28049578--28049652 Score: 55
Period size: 15 Copynumber: 5.5 Consensus size: 13
28049568 TAGTCACTTT
28049578 TATT-TATTTT-A
1 TATTATATTTTAA
*
28049589 TATTTTATTTTAA
1 TATTATATTTTAA
*
28049602 TTATTTATATTTAAAA
1 -TA-TTATATTT-TAA
28049618 TATTATATTTTAA
1 TATTATATTTTAA
* *
28049631 TCACTTATGTTATAA
1 T-A-TTATATTTTAA
28049646 TATTATA
1 TATTATA
28049653 ATATTTTAGT
Statistics
Matches: 51, Mismatches: 6, Indels: 12
0.74 0.09 0.17
Matches are distributed among these distances:
11 4 0.08
12 6 0.12
13 8 0.16
14 12 0.24
15 19 0.37
16 2 0.04
ACGTcount: A:0.36, C:0.03, G:0.01, T:0.60
Consensus pattern (13 bp):
TATTATATTTTAA
Found at i:28049638 original size:29 final size:28
Alignment explanation
Indices: 28049588--28049652 Score: 76
Period size: 29 Copynumber: 2.3 Consensus size: 28
28049578 TATTTATTTT
* * * *
28049588 ATATTTTATTTTAATTATTTATATTTAAA
1 ATATTATATTTTAATCACTTAT-GTTAAA
*
28049617 ATATTATATTTTAATCACTTATGTTATA
1 ATATTATATTTTAATCACTTATGTTAAA
28049645 ATATTATA
1 ATATTATA
28049653 ATATTTTAGT
Statistics
Matches: 31, Mismatches: 5, Indels: 1
0.84 0.14 0.03
Matches are distributed among these distances:
28 12 0.39
29 19 0.61
ACGTcount: A:0.38, C:0.03, G:0.02, T:0.57
Consensus pattern (28 bp):
ATATTATATTTTAATCACTTATGTTAAA
Found at i:28051176 original size:3 final size:3
Alignment explanation
Indices: 28051168--28051198 Score: 62
Period size: 3 Copynumber: 10.3 Consensus size: 3
28051158 TATTGAGGAG
28051168 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
1 TAA TAA TAA TAA TAA TAA TAA TAA TAA TAA T
28051199 TAAGAAGTAG
Statistics
Matches: 28, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 28 1.00
ACGTcount: A:0.65, C:0.00, G:0.00, T:0.35
Consensus pattern (3 bp):
TAA
Found at i:28051691 original size:16 final size:16
Alignment explanation
Indices: 28051670--28051702 Score: 66
Period size: 16 Copynumber: 2.1 Consensus size: 16
28051660 TTTTTGGTTC
28051670 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
28051686 GCTGTAATGGAATAGA
1 GCTGTAATGGAATAGA
28051702 G
1 G
28051703 GCATAATAGT
Statistics
Matches: 17, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
16 17 1.00
ACGTcount: A:0.36, C:0.06, G:0.33, T:0.24
Consensus pattern (16 bp):
GCTGTAATGGAATAGA
Found at i:28052141 original size:16 final size:16
Alignment explanation
Indices: 28052120--28052159 Score: 53
Period size: 16 Copynumber: 2.5 Consensus size: 16
28052110 TTTGGTTCGC
*
28052120 TGTAATAGAATAGATG
1 TGTAATAGAATAGAGG
*
28052136 TGTAATGGAATAGAGG
1 TGTAATAGAATAGAGG
*
28052152 CGTAATAG
1 TGTAATAG
28052160 GTAATTCTTT
Statistics
Matches: 20, Mismatches: 4, Indels: 0
0.83 0.17 0.00
Matches are distributed among these distances:
16 20 1.00
ACGTcount: A:0.40, C:0.03, G:0.30, T:0.28
Consensus pattern (16 bp):
TGTAATAGAATAGAGG
Found at i:28052221 original size:44 final size:46
Alignment explanation
Indices: 28052139--28052227 Score: 146
Period size: 44 Copynumber: 2.0 Consensus size: 46
28052129 ATAGATGTGT
* *
28052139 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
28052185 AATGAAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGGTTGAATG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATG
28052228 TAATAGAGGT
Statistics
Matches: 41, Mismatches: 2, Indels: 2
0.91 0.04 0.04
Matches are distributed among these distances:
44 20 0.49
45 3 0.07
46 18 0.44
ACGTcount: A:0.28, C:0.04, G:0.30, T:0.37
Consensus pattern (46 bp):
AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTGAATGG
Found at i:28052227 original size:39 final size:44
Alignment explanation
Indices: 28052139--28052244 Score: 123
Period size: 39 Copynumber: 2.5 Consensus size: 44
28052129 ATAGATGTGT
* *
28052139 AATGGAATAGAGGCGTAATAGGTAATTCTTTTGTTTGGTTGAATGG
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTT--ATGG
28052185 AATGAAATAGAGGCGTAAT-GGT-ATTCTTGTGTTTGG-T-T-G
1 AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
* *
28052224 AATGTAATAGAGGTGTAATAG
1 AATGAAATAGAGGCGTAATAG
28052245 CATAAGGAAA
Statistics
Matches: 55, Mismatches: 4, Indels: 8
0.82 0.06 0.12
Matches are distributed among these distances:
39 18 0.33
40 2 0.04
43 1 0.02
44 13 0.24
45 3 0.05
46 18 0.33
ACGTcount: A:0.30, C:0.04, G:0.30, T:0.36
Consensus pattern (44 bp):
AATGAAATAGAGGCGTAATAGGTAATTCTTGTGTTTGGTTATGG
Found at i:28052400 original size:26 final size:26
Alignment explanation
Indices: 28052371--28052483 Score: 63
Period size: 26 Copynumber: 4.2 Consensus size: 26
28052361 TTAATCATAT
28052371 TTTAACATAATTATTATTAAATATAA
1 TTTAACATAATTATTATTAAATATAA
* * * *
28052397 TTTAATA-AAATA-TA-TAAATTTAC
1 TTTAACATAATTATTATTAAATATAA
**
28052420 TAAAATCATAATATATGATACTATATAATATAA
1 TTTAA-CATAAT-TAT--TA-T-TA-AATATAA
*
28052453 TTTGAA-ATAATTATTATTAAATATAT
1 TTT-AACATAATTATTATTAAATATAA
28052479 TTTAA
1 TTTAA
28052484 TTAAAATATA
Statistics
Matches: 63, Mismatches: 13, Indels: 23
0.64 0.13 0.23
Matches are distributed among these distances:
23 10 0.16
24 3 0.05
25 8 0.13
26 17 0.27
27 2 0.03
28 1 0.02
29 4 0.06
31 3 0.05
32 7 0.11
33 6 0.10
34 2 0.03
ACGTcount: A:0.50, C:0.04, G:0.02, T:0.44
Consensus pattern (26 bp):
TTTAACATAATTATTATTAAATATAA
Found at i:28052418 original size:18 final size:17
Alignment explanation
Indices: 28052391--28052507 Score: 59
Period size: 18 Copynumber: 7.0 Consensus size: 17
28052381 TTATTATTAA
28052391 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
*
28052408 ATATAAATTTACTAAAAT
1 ATAT-AATTTAATAAAAT
* * * *
28052426 -CATAATAT-ATGATACT
1 ATATAATTTAAT-AAAAT
* *
28052442 ATATAATATAATTTGAAAT
1 ATATAATTTAA--TAAAAT
* *
28052461 A-ATTA-TT-ATTAAAT
1 ATATAATTTAATAAAAT
28052475 ATAT--TTTAATTAAAAT
1 ATATAATTTAA-TAAAAT
28052491 ATATAATTTAATAAAAT
1 ATATAATTTAATAAAAT
28052508 TCTTAATAAT
Statistics
Matches: 74, Mismatches: 14, Indels: 24
0.66 0.12 0.21
Matches are distributed among these distances:
14 8 0.11
15 4 0.05
16 17 0.23
17 20 0.27
18 21 0.28
19 3 0.04
20 1 0.01
ACGTcount: A:0.53, C:0.03, G:0.02, T:0.43
Consensus pattern (17 bp):
ATATAATTTAATAAAAT
Found at i:28056900 original size:17 final size:17
Alignment explanation
Indices: 28056878--28056911 Score: 52
Period size: 17 Copynumber: 2.0 Consensus size: 17
28056868 GTTCCTGGAT
28056878 TTTCTTCCTAA-TCTAAA
1 TTTCTTCC-AAGTCTAAA
28056895 TTTCTTCCAAGTCTAAA
1 TTTCTTCCAAGTCTAAA
28056912 CCTCCATCAT
Statistics
Matches: 16, Mismatches: 0, Indels: 2
0.89 0.00 0.11
Matches are distributed among these distances:
16 2 0.12
17 14 0.88
ACGTcount: A:0.29, C:0.24, G:0.03, T:0.44
Consensus pattern (17 bp):
TTTCTTCCAAGTCTAAA
Found at i:28058711 original size:24 final size:24
Alignment explanation
Indices: 28058663--28058711 Score: 71
Period size: 24 Copynumber: 2.0 Consensus size: 24
28058653 TTTTGAGTAA
*
28058663 TTTAAATTTTTTTCTTTTATGTTT
1 TTTAAATTTTTTTCTTTTATATTT
* *
28058687 TTTAACTTTTTTTCTTTTTTATTT
1 TTTAAATTTTTTTCTTTTATATTT
28058711 T
1 T
28058712 CCATTCTCTT
Statistics
Matches: 22, Mismatches: 3, Indels: 0
0.88 0.12 0.00
Matches are distributed among these distances:
24 22 1.00
ACGTcount: A:0.14, C:0.06, G:0.02, T:0.78
Consensus pattern (24 bp):
TTTAAATTTTTTTCTTTTATATTT
Found at i:28064298 original size:17 final size:17
Alignment explanation
Indices: 28064253--28064299 Score: 51
Period size: 17 Copynumber: 2.8 Consensus size: 17
28064243 ATAAGCAAAA
* *
28064253 AAAATTAGTTTTTGCTC
1 AAAAGTAGTTTTTGCCC
*
28064270 AAAAGTACTTTTTGGCCC
1 AAAAGTAGTTTTT-GCCC
28064288 AAAAGT-GTTTTT
1 AAAAGTAGTTTTT
28064300 AAGAAGCGAT
Statistics
Matches: 25, Mismatches: 4, Indels: 2
0.81 0.13 0.06
Matches are distributed among these distances:
17 16 0.64
18 9 0.36
ACGTcount: A:0.30, C:0.13, G:0.15, T:0.43
Consensus pattern (17 bp):
AAAAGTAGTTTTTGCCC
Found at i:28069754 original size:153 final size:153
Alignment explanation
Indices: 28069477--28070297 Score: 1129
Period size: 153 Copynumber: 5.4 Consensus size: 153
28069467 CAATTGTTTG
* * * ** * *
28069477 TATTTTGGCTCTTTATTCGTATTTTTTCTCAAATTTTATTACTTT-TA-AAAAATATACTATTTT
1 TATTTCGGCCCTTTATTCGTATTTTTTTTCGGATTTTATTACTTTCAATAAAAATATATTATTTT
*
28069540 C-TAATTTTATTATTTTAAATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTT
66 CGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTT
28069604 TTTATTTAAATTTAAAAAAACCCT
130 TTTATTTAAATTTAAAAAAACCCT
*
28069628 TATTTCGGCCCTTTATTCGTATTTTTTTTCAGATTTTATTACTTTCAATAAAAATATATTATTTT
1 TATTTCGGCCCTTTATTCGTATTTTTTTTCGGATTTTATTACTTTCAATAAAAATATATTATTTT
* * * *
28069693 CGTATTTTATTATTTTACATTATTTTAGTACATTATTTTTGAAATATATTAATTTACTGTGTTTT
66 CGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
** * *
28069758 TTAAATAAATTAAAAAAAACCTT
131 TTATTTAAATTTAAAAAAACCCT
* * * * * *
28069781 TATTTCGACCATTTGTTAGTATTTTTTTCCGGATTTTATTACTTCCAATAAAAATATATTATTTT
1 TATTTCGGCCCTTTATTCGTATTTTTTTTCGGATTTTATTACTTTCAATAAAAATATATTATTTT
* * * *
28069846 CGTATTTTATTAGTTTACATTATTTTAGTACATTATATTTGAAATGTATTAATTTATTGTGTTTT
66 CGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
** *
28069911 TTAAATAAATTTTAAAAAAACCAT
131 TTATTTAAA-TTTAAAAAAACCCT
* *
28069935 TATTTCGGCCCTTTGTTCGTATTTTTTTTCCGGATTTTATTACTTT-TA-AAAAATATATTATTT
1 TATTTCGGCCCTTTATTCGTATTTTTTTT-CGGATTTTATTACTTTCAATAAAAATATATTATTT
28069998 TC-TAATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTT
65 TCGT-ATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTT
28070062 TTTTATTTAAATTTAAAAAAA-CCT
129 TTTTATTTAAATTTAAAAAAACCCT
** * *
28070086 TATTTCAACCATTTATTCGTA--TTTTTTCGGATTTTATTACTTTTAATAAAAATATATTATTTT
1 TATTTCGGCCCTTTATTCGTATTTTTTTTCGGATTTTATTACTTTCAATAAAAATATATTATTTT
28070149 CGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
66 CGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTG-TTT
*
28070214 TTTATTTAAATTAAAAAAAAACCCT
130 TTTATTTAAATT-TAAAAAAACCCT
* *
28070239 TATTTCAGCCCTTTGTTGTTCGTATTTTTTTTACCGGATTTTATTACTTTCAATAAAAA
1 TATTTCGGCCC--T-TTATTCGTATTTTTTTT--CGGATTTTATTACTTTCAATAAAAA
28070298 AACACACTAA
Statistics
Matches: 600, Mismatches: 51, Indels: 29
0.88 0.08 0.04
Matches are distributed among these distances:
148 16 0.03
149 7 0.01
150 75 0.12
151 76 0.13
152 19 0.03
153 314 0.52
154 39 0.06
155 16 0.03
156 8 0.01
158 6 0.01
160 24 0.04
ACGTcount: A:0.30, C:0.09, G:0.07, T:0.53
Consensus pattern (153 bp):
TATTTCGGCCCTTTATTCGTATTTTTTTTCGGATTTTATTACTTTCAATAAAAATATATTATTTT
CGTATTTTATTATTTTACATTATTTTAGTACATTATGTTTGAAATGTATTCATTTAGTGTGTTTT
TTATTTAAATTTAAAAAAACCCT
Found at i:28072268 original size:43 final size:42
Alignment explanation
Indices: 28072164--28072401 Score: 198
Period size: 42 Copynumber: 5.6 Consensus size: 42
28072154 ATCTGTTACT
* *
28072164 CGGTGGATTCAGCACTTAGCAACCACTTTA-AATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTTACAA-TCAGTGATA
*
28072206 CGG-GGAATCAGCACATAGCAACCCCTTTCACAATCAAG-GATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTT-ACAATC-AGTGATA
* * * *
28072248 CGGTGGAATCAACACTTAGCAACCACCTATATATTCAGTGATA
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTACAATCAGTGATA
* **
28072291 CGG-GGAATCAGCACGTAGCAACCCCTTTCACAATCAAAGATA
1 CGGTGGAATCAGCACTTAGCAACCCCTTT-ACAATCAGTGATA
* ** * * * * * * *
28072333 TGGTGGAATTTGAACTTAACAACCACCTTTAGAGTCAATAATT
1 CGGTGGAATCAGCACTTAGCAACC-CCTTTACAATCAGTGATA
*
28072376 TGG-GGAATCAGCACTTAGCAACCCCT
1 CGGTGGAATCAGCACTTAGCAACCCCT
28072402 CGGGGAATCT
Statistics
Matches: 157, Mismatches: 30, Indels: 19
0.76 0.15 0.09
Matches are distributed among these distances:
41 29 0.18
42 60 0.38
43 59 0.38
44 9 0.06
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (42 bp):
CGGTGGAATCAGCACTTAGCAACCCCTTTACAATCAGTGATA
Found at i:28072310 original size:85 final size:85
Alignment explanation
Indices: 28072164--28072401 Score: 300
Period size: 85 Copynumber: 2.8 Consensus size: 85
28072154 ATCTGTTACT
* *
28072164 CGGTGGATTCAGCACTTAGCAACCA-CTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
1 CGGTGGAATCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
*
28072228 CCCTTTCACAATCAAGGATA
66 CCCTTTCACAATCAAAGATA
* * *
28072248 CGGTGGAATCAACACTTAGCAACCACCTATATATTCAGTGATACGGGGAATCAGCACGTAGCAAC
1 CGGTGGAATCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
28072313 CCCTTTCACAATCAAAGATA
66 CCCTTTCACAATCAAAGATA
* ** * * * * * ** *
28072333 TGGTGGAATTTGA-ACTTAACAACCACCTTTAGAGTCAATAATTTGGGGAATCAGCACTTAGCAA
1 CGGTGGAA-TCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAA
28072397 CCCCT
65 CCCCT
28072402 CGGGGAATCT
Statistics
Matches: 134, Mismatches: 18, Indels: 3
0.86 0.12 0.02
Matches are distributed among these distances:
84 23 0.17
85 109 0.81
86 2 0.01
ACGTcount: A:0.34, C:0.24, G:0.18, T:0.24
Consensus pattern (85 bp):
CGGTGGAATCAACACTTAGCAACCACCTTTAAATTCAGTGATACGGGGAATCAGCACATAGCAAC
CCCTTTCACAATCAAAGATA
Found at i:28072406 original size:26 final size:26
Alignment explanation
Indices: 28072377--28072427 Score: 84
Period size: 26 Copynumber: 2.0 Consensus size: 26
28072367 TCAATAATTT
28072377 GGGGAATCAGCACTTAGCAACCCCTC
1 GGGGAATCAGCACTTAGCAACCCCTC
* *
28072403 GGGGAATCTGCACTTAGCGACCCCT
1 GGGGAATCAGCACTTAGCAACCCCT
28072428 TTTTATTCAA
Statistics
Matches: 23, Mismatches: 2, Indels: 0
0.92 0.08 0.00
Matches are distributed among these distances:
26 23 1.00
ACGTcount: A:0.24, C:0.33, G:0.25, T:0.18
Consensus pattern (26 bp):
GGGGAATCAGCACTTAGCAACCCCTC
Found at i:28073871 original size:25 final size:24
Alignment explanation
Indices: 28073837--28073885 Score: 89
Period size: 25 Copynumber: 2.0 Consensus size: 24
28073827 TAAAATACTT
28073837 CTGTACACTCTTTCACTAGAACAC
1 CTGTACACTCTTTCACTAGAACAC
28073861 NCTGTACACTCTTTCACTAGAACAC
1 -CTGTACACTCTTTCACTAGAACAC
28073886 TCTTTAAACA
Statistics
Matches: 24, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
25 24 1.00
ACGTcount: A:0.29, C:0.33, G:0.08, T:0.29
Consensus pattern (24 bp):
CTGTACACTCTTTCACTAGAACAC
Found at i:28078900 original size:15 final size:15
Alignment explanation
Indices: 28078853--28078903 Score: 52
Period size: 15 Copynumber: 3.5 Consensus size: 15
28078843 TTACTTAAGG
28078853 TTACATTTTAGTCAC
1 TTACATTTTAGTCAC
* * *
28078868 TTATATTTAAAAT-A-
1 TTACATTT-TAGTCAC
28078882 TTACATTTTAGTCAC
1 TTACATTTTAGTCAC
28078897 TTACATT
1 TTACATT
28078904 AACGAGTTGT
Statistics
Matches: 27, Mismatches: 6, Indels: 6
0.69 0.15 0.15
Matches are distributed among these distances:
13 2 0.07
14 8 0.30
15 15 0.56
16 2 0.07
ACGTcount: A:0.33, C:0.14, G:0.04, T:0.49
Consensus pattern (15 bp):
TTACATTTTAGTCAC
Found at i:28083854 original size:53 final size:54
Alignment explanation
Indices: 28083796--28083905 Score: 152
Period size: 53 Copynumber: 2.1 Consensus size: 54
28083786 CCATGACACT
*
28083796 AAAGAAGACCATATCGTGTAAGACCATAACTT-GTGGGTTATGGCATCATATG-G
1 AAAGAAGACCATATCGTGTAAGACCATAA-TTGGTGGGTTATGACATCATATGAG
* * * *
28083849 AAAGAATACCATATTGTGTAAGATCGTAATTGGTGGGTTATGACATCATATGAG
1 AAAGAAGACCATATCGTGTAAGACCATAATTGGTGGGTTATGACATCATATGAG
28083903 AAA
1 AAA
28083906 ATTTAAGGAA
Statistics
Matches: 50, Mismatches: 5, Indels: 3
0.86 0.09 0.05
Matches are distributed among these distances:
52 2 0.04
53 44 0.88
54 4 0.08
ACGTcount: A:0.36, C:0.12, G:0.24, T:0.28
Consensus pattern (54 bp):
AAAGAAGACCATATCGTGTAAGACCATAATTGGTGGGTTATGACATCATATGAG
Found at i:28084122 original size:29 final size:28
Alignment explanation
Indices: 28084078--28084133 Score: 76
Period size: 29 Copynumber: 2.0 Consensus size: 28
28084068 ATTGAATGTT
* *
28084078 AAGGAATGCCTTTGTGGCAAACCTCTAG
1 AAGGAATGCCTCTGTGACAAACCTCTAG
*
28084106 AAGGAAATGCCTCTGTGACAAATCTCTA
1 AAGG-AATGCCTCTGTGACAAACCTCTA
28084134 AACATGGAAG
Statistics
Matches: 24, Mismatches: 3, Indels: 1
0.86 0.11 0.04
Matches are distributed among these distances:
28 4 0.17
29 20 0.83
ACGTcount: A:0.32, C:0.21, G:0.21, T:0.25
Consensus pattern (28 bp):
AAGGAATGCCTCTGTGACAAACCTCTAG
Found at i:28088752 original size:26 final size:26
Alignment explanation
Indices: 28088716--28088791 Score: 118
Period size: 26 Copynumber: 3.0 Consensus size: 26
28088706 AGGCAAACTT
* *
28088716 GTCAAAATTTTGCTAGGGGTAAAATC
1 GTCAAAGTTTTACTAGGGGTAAAATC
*
28088742 GTTAAAGTTTTACTAGGGGTAAAATC
1 GTCAAAGTTTTACTAGGGGTAAAATC
28088768 GTCAAAGTTTTACTA-GGGTAAAAT
1 GTCAAAGTTTTACTAGGGGTAAAAT
28088792 AGGGATAATT
Statistics
Matches: 46, Mismatches: 4, Indels: 1
0.90 0.08 0.02
Matches are distributed among these distances:
25 9 0.20
26 37 0.80
ACGTcount: A:0.36, C:0.09, G:0.22, T:0.33
Consensus pattern (26 bp):
GTCAAAGTTTTACTAGGGGTAAAATC
Found at i:28106227 original size:13 final size:13
Alignment explanation
Indices: 28106209--28106235 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28106199 TTAATTTATA
28106209 TGTGTGAAAATTT
1 TGTGTGAAAATTT
28106222 TGTGTGAAAATTT
1 TGTGTGAAAATTT
28106235 T
1 T
28106236 ATCGTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:28107416 original size:42 final size:43
Alignment explanation
Indices: 28107315--28107431 Score: 125
Period size: 42 Copynumber: 2.7 Consensus size: 43
28107305 ATATGATATT
* * *
28107315 GTGTAAGACCACGTCT-GAGAC-GTTGGCATCGATTTGAGATTTAC
1 GTGTAAGACCATGTCTAG-GACAG-TGGCATCG-TATAAGATTTAC
28107359 GTGTAAGACCATGTCTAGGACA-TCGGCATCGTATAAGATTT-C
1 GTGTAAGACCATGTCTAGGACAGT-GGCATCGTATAAGATTTAC
* *
28107401 GTGTAAGACCCTGTCTGGGACAGTGGCATCG
1 GTGTAAGACCATGTCTAGGACAGTGGCATCG
28107432 CTATTGGTTT
Statistics
Matches: 64, Mismatches: 5, Indels: 10
0.81 0.06 0.13
Matches are distributed among these distances:
42 28 0.44
43 10 0.16
44 25 0.39
45 1 0.02
ACGTcount: A:0.25, C:0.20, G:0.28, T:0.27
Consensus pattern (43 bp):
GTGTAAGACCATGTCTAGGACAGTGGCATCGTATAAGATTTAC
Found at i:28110473 original size:18 final size:19
Alignment explanation
Indices: 28110450--28110486 Score: 58
Period size: 19 Copynumber: 2.0 Consensus size: 19
28110440 TGTAATTTGG
28110450 TTTGGTTA-TTTTACTTAA
1 TTTGGTTAGTTTTACTTAA
*
28110468 TTTGGTTAGTTTTATTTAA
1 TTTGGTTAGTTTTACTTAA
28110487 CTTAGTTTAC
Statistics
Matches: 17, Mismatches: 1, Indels: 1
0.89 0.05 0.05
Matches are distributed among these distances:
18 8 0.47
19 9 0.53
ACGTcount: A:0.22, C:0.03, G:0.14, T:0.62
Consensus pattern (19 bp):
TTTGGTTAGTTTTACTTAA
Found at i:28110485 original size:23 final size:24
Alignment explanation
Indices: 28110442--28110490 Score: 57
Period size: 23 Copynumber: 2.1 Consensus size: 24
28110432 CAACTTGGTG
*
28110442 TAATTTGGTTTGGTTATTTT-ACT
1 TAATTTGGTTAGGTTATTTTAACT
*
28110465 TAATTTGGTTA-GTTTTATTTAACT
1 TAATTTGGTTAGGTTAT-TTTAACT
28110489 TA
1 TA
28110491 GTTTACTTTA
Statistics
Matches: 22, Mismatches: 2, Indels: 3
0.81 0.07 0.11
Matches are distributed among these distances:
22 4 0.18
23 13 0.59
24 5 0.23
ACGTcount: A:0.22, C:0.04, G:0.14, T:0.59
Consensus pattern (24 bp):
TAATTTGGTTAGGTTATTTTAACT
Found at i:28114226 original size:42 final size:41
Alignment explanation
Indices: 28114110--28114250 Score: 149
Period size: 41 Copynumber: 3.3 Consensus size: 41
28114100 GTCCAAAAAT
* * *
28114110 ATTTTTTTCTTTTCAAAATTTAAATTACAAACTAATTAATTTC
1 ATTTTTTTCTTAT-AAAATTTAAATAAC-AACTTATTAATTTC
* * *
28114153 TTTTTTTTCTTGT-AAATTTAAATAAAAAACTTATTAATTTC
1 ATTTTTTTCTTATAAAATTTAAAT-AACAACTTATTAATTTC
*
28114194 ATTTGTTTCTTATAAAATTTAAAATAACAACTTATTAATTTC
1 ATTTTTTTCTTATAAAATTT-AAATAACAACTTATTAATTTC
*
28114236 ACTTCTTTTTTTTAT
1 A-TT-TTTTTCTTAT
28114251 TTCATATCTA
Statistics
Matches: 82, Mismatches: 11, Indels: 9
0.80 0.11 0.09
Matches are distributed among these distances:
41 33 0.40
42 24 0.29
43 17 0.21
44 8 0.10
ACGTcount: A:0.35, C:0.10, G:0.01, T:0.53
Consensus pattern (41 bp):
ATTTTTTTCTTATAAAATTTAAATAACAACTTATTAATTTC
Found at i:28117684 original size:21 final size:21
Alignment explanation
Indices: 28117652--28117694 Score: 61
Period size: 21 Copynumber: 2.0 Consensus size: 21
28117642 ATATAAATAA
*
28117652 AATAATAAATATGTAATTGTAT
1 AATAATAAATATATAATT-TAT
28117674 AATAA-AAATATATAATTTAT
1 AATAATAAATATATAATTTAT
28117694 A
1 A
28117695 TATATCATTA
Statistics
Matches: 20, Mismatches: 1, Indels: 2
0.87 0.04 0.09
Matches are distributed among these distances:
20 4 0.20
21 11 0.55
22 5 0.25
ACGTcount: A:0.56, C:0.00, G:0.05, T:0.40
Consensus pattern (21 bp):
AATAATAAATATATAATTTAT
Found at i:28118801 original size:13 final size:13
Alignment explanation
Indices: 28118783--28118809 Score: 54
Period size: 13 Copynumber: 2.1 Consensus size: 13
28118773 TTAATTTATA
28118783 TGTGTGAAAATTT
1 TGTGTGAAAATTT
28118796 TGTGTGAAAATTT
1 TGTGTGAAAATTT
28118809 T
1 T
28118810 ATCGTTTGTG
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
13 14 1.00
ACGTcount: A:0.30, C:0.00, G:0.22, T:0.48
Consensus pattern (13 bp):
TGTGTGAAAATTT
Found at i:28119955 original size:44 final size:43
Alignment explanation
Indices: 28119890--28120030 Score: 137
Period size: 42 Copynumber: 3.3 Consensus size: 43
28119880 ATATATGATA
* *
28119890 TCGTGTAAGACCACGTCTGGGATGTTGGCATCGATTTGAGATT
1 TCGTGTAAGACCATGTCTGGGAAGTTGGCATCGATTTGAGATT
* * * *
28119933 TATGTGTAAGACCATGTCTGGGACA-TTGACATCG-TATAAGATT
1 T-CGTGTAAGACCATGTCTGGGA-AGTTGGCATCGATTTGAGATT
*
28119976 TCGTGTAAGACCTTGTCTGGGACAG-TGGCATCGATATTG-GATT
1 TCGTGTAAGACCATGTCTGGGA-AGTTGGCATCGAT-TTGAGATT
* *
28120019 ACATGTAAGACC
1 TCGTGTAAGACC
28120031 TCGTCTGTGA
Statistics
Matches: 80, Mismatches: 13, Indels: 10
0.78 0.13 0.10
Matches are distributed among these distances:
42 28 0.35
43 24 0.30
44 28 0.35
ACGTcount: A:0.26, C:0.16, G:0.27, T:0.31
Consensus pattern (43 bp):
TCGTGTAAGACCATGTCTGGGAAGTTGGCATCGATTTGAGATT
Found at i:28119993 original size:42 final size:43
Alignment explanation
Indices: 28119880--28120037 Score: 147
Period size: 43 Copynumber: 3.7 Consensus size: 43
28119870 AGGAAATCTA
* * **
28119880 ATATATGATATCGTGTAAGACCACGTCTGGGATGTTGGCATCG
1 ATATAAGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCG
* * * * *
28119923 ATTTGAGATTTATGTGTAAGACCATGTCTGGGACATTGACATCG
1 ATATAAGATTT-CGTGTAAGACCACGTCTGGGACATTGGCATCG
** *
28119967 -TATAAGATTTCGTGTAAGACCTTGTCTGGGACAGTGGCATCG
1 ATATAAGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCG
** * * *
28120009 ATATTGGATTACATGTAAGACCTCGTCTG
1 ATATAAGATTTCGTGTAAGACCACGTCTG
28120038 TGACGTATGC
Statistics
Matches: 93, Mismatches: 20, Indels: 4
0.79 0.17 0.03
Matches are distributed among these distances:
42 28 0.30
43 38 0.41
44 27 0.29
ACGTcount: A:0.26, C:0.16, G:0.26, T:0.32
Consensus pattern (43 bp):
ATATAAGATTTCGTGTAAGACCACGTCTGGGACATTGGCATCG
Found at i:28133446 original size:96 final size:96
Alignment explanation
Indices: 28133339--28133523 Score: 298
Period size: 96 Copynumber: 1.9 Consensus size: 96
28133329 GAGGAATACA
* *
28133339 ATTGAGCTATCACCTTTTGTGAAATGTTATTGGTCTAGTTCAAAAGATCATAAGGGTTTCCAATG
1 ATTGAGATATCACCTTTTATGAAATGTTATTGGTCTAGTTCAAAAGATCATAAGGGTTTCCAATG
*
28133404 TCCAATTAAATATCCAAATAGAGAGAATATG
66 TCCAATGAAATATCCAAATAGAGAGAATATG
* * * *
28133435 ATTGAGATATCACCTTTTATGCAATGTTATTGGTGTAGTTCAAAAGATCATAATGGTTTCCAATT
1 ATTGAGATATCACCTTTTATGAAATGTTATTGGTCTAGTTCAAAAGATCATAAGGGTTTCCAATG
*
28133500 TCCAATGAAATATCCAACTAGAGA
66 TCCAATGAAATATCCAAATAGAGA
28133524 AAAAAGTAAG
Statistics
Matches: 81, Mismatches: 8, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
96 81 1.00
ACGTcount: A:0.35, C:0.14, G:0.17, T:0.34
Consensus pattern (96 bp):
ATTGAGATATCACCTTTTATGAAATGTTATTGGTCTAGTTCAAAAGATCATAAGGGTTTCCAATG
TCCAATGAAATATCCAAATAGAGAGAATATG
Found at i:28139764 original size:25 final size:25
Alignment explanation
Indices: 28139736--28139830 Score: 81
Period size: 25 Copynumber: 3.8 Consensus size: 25
28139726 TCATGTGCAT
*
28139736 GTATGCTCATACGAGTTGTGAATCG
1 GTATGCTCATACGAGCTGTGAATCG
*
28139761 GTATGCTCACT-TGA-CT-TGTAGATCG
1 GTATGCTCA-TACGAGCTGTG-A-ATCG
* *
28139786 GTATGCTC-TCACGAGCTATAAATCG
1 GTATGCTCAT-ACGAGCTGTGAATCG
*
28139811 GTATGCTCAAACGAGCTGTG
1 GTATGCTCATACGAGCTGTG
28139831 GGTCGGAACA
Statistics
Matches: 55, Mismatches: 7, Indels: 16
0.71 0.09 0.21
Matches are distributed among these distances:
23 3 0.05
24 2 0.04
25 45 0.82
26 4 0.07
27 1 0.02
ACGTcount: A:0.24, C:0.20, G:0.25, T:0.31
Consensus pattern (25 bp):
GTATGCTCATACGAGCTGTGAATCG
Found at i:28142678 original size:22 final size:22
Alignment explanation
Indices: 28142653--28142694 Score: 57
Period size: 22 Copynumber: 1.9 Consensus size: 22
28142643 CGAAGTGTAG
* *
28142653 AACAGTAAGCACTGAAGTGCGA
1 AACAATAAGCACTAAAGTGCGA
*
28142675 AACAATAAGCGCTAAAGTGC
1 AACAATAAGCACTAAAGTGC
28142695 AAGACGGTAA
Statistics
Matches: 17, Mismatches: 3, Indels: 0
0.85 0.15 0.00
Matches are distributed among these distances:
22 17 1.00
ACGTcount: A:0.43, C:0.19, G:0.24, T:0.14
Consensus pattern (22 bp):
AACAATAAGCACTAAAGTGCGA
Found at i:28143419 original size:11 final size:11
Alignment explanation
Indices: 28143405--28143447 Score: 52
Period size: 11 Copynumber: 3.8 Consensus size: 11
28143395 AGTAAAAATT
28143405 AATAAAATATA
1 AATAAAATATA
28143416 AAT-AAATATCA
1 AATAAAATAT-A
*
28143427 AATCAAAATATT
1 AAT-AAAATATA
28143439 AATAAAATA
1 AATAAAATA
28143448 ATATTTACCT
Statistics
Matches: 28, Mismatches: 1, Indels: 6
0.80 0.03 0.17
Matches are distributed among these distances:
10 6 0.21
11 13 0.46
12 3 0.11
13 6 0.21
ACGTcount: A:0.67, C:0.05, G:0.00, T:0.28
Consensus pattern (11 bp):
AATAAAATATA
Found at i:28152477 original size:19 final size:19
Alignment explanation
Indices: 28152453--28152489 Score: 65
Period size: 19 Copynumber: 1.9 Consensus size: 19
28152443 AAATAACTCT
28152453 TTATAATTTTTACAATTTG
1 TTATAATTTTTACAATTTG
*
28152472 TTATAATTTTTGCAATTT
1 TTATAATTTTTACAATTT
28152490 ATATGTTTTT
Statistics
Matches: 17, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
19 17 1.00
ACGTcount: A:0.30, C:0.05, G:0.05, T:0.59
Consensus pattern (19 bp):
TTATAATTTTTACAATTTG
Found at i:28152511 original size:10 final size:10
Alignment explanation
Indices: 28152496--28152548 Score: 54
Period size: 10 Copynumber: 5.4 Consensus size: 10
28152486 ATTTATATGT
28152496 TTTTTTAATA
1 TTTTTTAATA
**
28152506 TTTTTTCTTA
1 TTTTTTAATA
*
28152516 TTTTTTACTA
1 TTTTTTAATA
* *
28152526 -TTTTCAACA
1 TTTTTTAATA
28152535 TTTTTTAATA
1 TTTTTTAATA
28152545 TTTT
1 TTTT
28152549 CTCTACAATT
Statistics
Matches: 33, Mismatches: 9, Indels: 2
0.75 0.20 0.05
Matches are distributed among these distances:
9 6 0.18
10 27 0.82
ACGTcount: A:0.23, C:0.08, G:0.00, T:0.70
Consensus pattern (10 bp):
TTTTTTAATA
Found at i:28152578 original size:9 final size:9
Alignment explanation
Indices: 28152564--28152630 Score: 59
Period size: 9 Copynumber: 7.6 Consensus size: 9
28152554 CAATTCTCTA
28152564 TATAATTTT
1 TATAATTTT
28152573 TATAATTATT
1 TATAATT-TT
* *
28152583 TTTCATTTAT
1 TATAATTT-T
28152593 TATAATTTT
1 TATAATTTT
28152602 TATAA--TT
1 TATAATTTT
* *
28152609 AAT-ATTAT
1 TATAATTTT
28152617 TATAATTTT
1 TATAATTTT
28152626 TATAA
1 TATAA
28152631 AATAAAAATT
Statistics
Matches: 45, Mismatches: 8, Indels: 10
0.71 0.13 0.16
Matches are distributed among these distances:
6 1 0.02
7 4 0.09
8 3 0.07
9 23 0.51
10 14 0.31
ACGTcount: A:0.37, C:0.01, G:0.00, T:0.61
Consensus pattern (9 bp):
TATAATTTT
Found at i:28154262 original size:19 final size:19
Alignment explanation
Indices: 28154207--28154256 Score: 75
Period size: 19 Copynumber: 2.6 Consensus size: 19
28154197 NNNNNACGCT
*
28154207 CTTCATGCGCCAAGATGCA
1 CTTCATGTGCCAAGATGCA
28154226 CTTCATGTGCCAAGATGCA
1 CTTCATGTGCCAAGATGCA
28154245 CCTT-ATGTGCCA
1 -CTTCATGTGCCA
28154257 GTATGCGTTC
Statistics
Matches: 29, Mismatches: 1, Indels: 2
0.91 0.03 0.06
Matches are distributed among these distances:
19 26 0.90
20 3 0.10
ACGTcount: A:0.24, C:0.30, G:0.20, T:0.26
Consensus pattern (19 bp):
CTTCATGTGCCAAGATGCA
Found at i:28166374 original size:102 final size:101
Alignment explanation
Indices: 28166182--28166366 Score: 248
Period size: 102 Copynumber: 1.8 Consensus size: 101
28166172 GAAAATATTT
* * * * *
28166182 AAAAAAATTTGAAGGAAAATGGGTTTGGGGTAGATAGGGGTGGGATGGGAGAGGAGTAAAAATTT
1 AAAAAAATTTGAAGGAAAATGGGTTTGGGGTAGATAGGGGTAGAATGAGAGAAGAGTAAAAATAT
**
28166247 TGGGGGAAAAGTGGGAAAGAGGGGGGAAATATTCAA
66 TGGGGGAAAAGTGAAAAAGAGGGGGGAAATATTCAA
** * *
28166283 AAAAAAATTTGTGGGGAAAATGGGTTTGGGGTAGATGGGGGTAGAATGAGAGAAGAGTAAAAGTA
1 AAAAAAATTTG-AAGGAAAATGGGTTTGGGGTAGATAGGGGTAGAATGAGAGAAGAGTAAAAATA
28166348 TTGGGGG-AAAGT-AAAAAGA
65 TTGGGGGAAAAGTGAAAAAGA
28166367 TTTGGGGGTT
Statistics
Matches: 72, Mismatches: 11, Indels: 3
0.84 0.13 0.03
Matches are distributed among these distances:
100 5 0.07
101 16 0.22
102 51 0.71
ACGTcount: A:0.40, C:0.01, G:0.39, T:0.20
Consensus pattern (101 bp):
AAAAAAATTTGAAGGAAAATGGGTTTGGGGTAGATAGGGGTAGAATGAGAGAAGAGTAAAAATAT
TGGGGGAAAAGTGAAAAAGAGGGGGGAAATATTCAA
Found at i:28168817 original size:15 final size:15
Alignment explanation
Indices: 28168797--28168825 Score: 58
Period size: 15 Copynumber: 1.9 Consensus size: 15
28168787 TCTCTTGTTT
28168797 ATTCTCTCATTCATC
1 ATTCTCTCATTCATC
28168812 ATTCTCTCATTCAT
1 ATTCTCTCATTCAT
28168826 TTCCCTATTA
Statistics
Matches: 14, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
15 14 1.00
ACGTcount: A:0.21, C:0.31, G:0.00, T:0.48
Consensus pattern (15 bp):
ATTCTCTCATTCATC
Found at i:28170814 original size:22 final size:23
Alignment explanation
Indices: 28170789--28170834 Score: 67
Period size: 22 Copynumber: 2.0 Consensus size: 23
28170779 ACTTATCTTA
28170789 TTCTGGCAGATT-ACTGCACTAT
1 TTCTGGCAGATTGACTGCACTAT
* *
28170811 TTCTGGCAGCTTGACTGCGCTAT
1 TTCTGGCAGATTGACTGCACTAT
28170834 T
1 T
28170835 CTAAAAAGTG
Statistics
Matches: 21, Mismatches: 2, Indels: 1
0.88 0.08 0.04
Matches are distributed among these distances:
22 11 0.52
23 10 0.48
ACGTcount: A:0.17, C:0.24, G:0.22, T:0.37
Consensus pattern (23 bp):
TTCTGGCAGATTGACTGCACTAT
Found at i:28170983 original size:30 final size:30
Alignment explanation
Indices: 28170947--28171070 Score: 117
Period size: 30 Copynumber: 4.1 Consensus size: 30
28170937 AGGGTAAGAT
*
28170947 CTGAATTTGTACATTTATCTGCATCTGTAA
1 CTGAATTTGTACATATATCTGCATCTGTAA
*
28170977 CTGAATTTGTATC-TATATTTGCATCTGTAA
1 CTGAATTTGTA-CATATATCTGCATCTGTAA
* * * *
28171007 CTGAATCTATA-TTAGTATCTGCATCAGTAA
1 CTGAATTTGTACATA-TATCTGCATCTGTAA
** * * *
28171037 CCAAATCTGAACCTATATCTGCATCTGTAA
1 CTGAATTTGTACATATATCTGCATCTGTAA
28171067 CTGA
1 CTGA
28171071 TCTGTCTGTT
Statistics
Matches: 76, Mismatches: 14, Indels: 8
0.78 0.14 0.08
Matches are distributed among these distances:
29 2 0.03
30 71 0.93
31 3 0.04
ACGTcount: A:0.30, C:0.19, G:0.13, T:0.39
Consensus pattern (30 bp):
CTGAATTTGTACATATATCTGCATCTGTAA
Found at i:28188128 original size:206 final size:206
Alignment explanation
Indices: 28187773--28188177 Score: 648
Period size: 206 Copynumber: 2.0 Consensus size: 206
28187763 CCTCCCTCCT
*
28187773 GACGCAATACATCTCACCTTACCTGAAACATAAATATAACATTTTTGTAAGTTCAAGAGAACTTA
1 GACGCAATACATCCCACCTTACCTGAAACATAAATATAACATTTTTGTAAGTTCAAGAGAACTTA
*
28187838 ATGAGCTTTAATCCAAAATATACCTTGGCGGATATTGATTATGATTAATGAACATCTGTGCACCA
66 ATGAGCTTTAATCCAAAATATACCTTGGCGAATATTGATTATGATTAATGAACATCTGTGCACCA
* * * *
28187903 ACTATTATTTTTCGACCACTTTCTTCTACCTCGGGCAGATACCACTACAGTTTTGGTATACAGTT
131 ACTATCATTTTTAGACCACTTTCTTCTACCTCGAGCAGATACCACTACAGTTTTGGTATACACTT
28187968 ACATGCCACCC
196 ACATGCCACCC
* * ** *
28187979 GACGCAATACATCCCACTTTACTTGAAACATAAATATAATTTTTTTGTAAGTTCAGGAGAACTTA
1 GACGCAATACATCCCACCTTACCTGAAACATAAATATAACATTTTTGTAAGTTCAAGAGAACTTA
* *
28188044 ATGAGCTTTAATCCAAAATATACCTTGGCTAATATTGATTATGATTAATGAACATCTGTGCCCCA
66 ATGAGCTTTAATCCAAAATATACCTTGGCGAATATTGATTATGATTAATGAACATCTGTGCACCA
* * ** *
28188109 ATTATCCTTTTTAGACCACTTTCTTCTACCTCGAGTGGATACCACTACAGTTTTTGTATACACTT
131 ACTATCATTTTTAGACCACTTTCTTCTACCTCGAGCAGATACCACTACAGTTTTGGTATACACTT
28188174 ACAT
196 ACAT
28188178 ACCAACTATC
Statistics
Matches: 181, Mismatches: 18, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
206 181 1.00
ACGTcount: A:0.32, C:0.21, G:0.13, T:0.34
Consensus pattern (206 bp):
GACGCAATACATCCCACCTTACCTGAAACATAAATATAACATTTTTGTAAGTTCAAGAGAACTTA
ATGAGCTTTAATCCAAAATATACCTTGGCGAATATTGATTATGATTAATGAACATCTGTGCACCA
ACTATCATTTTTAGACCACTTTCTTCTACCTCGAGCAGATACCACTACAGTTTTGGTATACACTT
ACATGCCACCC
Found at i:28188191 original size:22 final size:22
Alignment explanation
Indices: 28188166--28188211 Score: 58
Period size: 22 Copynumber: 2.1 Consensus size: 22
28188156 CAGTTTTTGT
28188166 ATACACTTA-CATACCAACTATC
1 ATACACTTATCATACCAA-TATC
**
28188188 ATACTTTTATCATACCAATATC
1 ATACACTTATCATACCAATATC
28188210 AT
1 AT
28188212 CCTTACCTAA
Statistics
Matches: 21, Mismatches: 2, Indels: 2
0.84 0.08 0.08
Matches are distributed among these distances:
22 13 0.62
23 8 0.38
ACGTcount: A:0.39, C:0.26, G:0.00, T:0.35
Consensus pattern (22 bp):
ATACACTTATCATACCAATATC
Found at i:28189144 original size:15 final size:15
Alignment explanation
Indices: 28189124--28189155 Score: 55
Period size: 15 Copynumber: 2.1 Consensus size: 15
28189114 CATTTCACTA
*
28189124 TTATGTCTTTTGTAT
1 TTATGTCTTTTATAT
28189139 TTATGTCTTTTATAT
1 TTATGTCTTTTATAT
28189154 TT
1 TT
28189156 TGCATGCACA
Statistics
Matches: 16, Mismatches: 1, Indels: 0
0.94 0.06 0.00
Matches are distributed among these distances:
15 16 1.00
ACGTcount: A:0.16, C:0.06, G:0.09, T:0.69
Consensus pattern (15 bp):
TTATGTCTTTTATAT
Found at i:28196922 original size:38 final size:39
Alignment explanation
Indices: 28196825--28196936 Score: 154
Period size: 38 Copynumber: 2.9 Consensus size: 39
28196815 TAAAAACATG
* * * *
28196825 TATTAAAGATGTCCAAACTATGACATAATTAAATACTCT
1 TATTAATGATGTTCAAATTATGACATAATTAAATACTCA
* * *
28196864 TATTAATGATATTTAGATTATGACATAATTAAA-ACTCA
1 TATTAATGATGTTCAAATTATGACATAATTAAATACTCA
28196902 TATTAATGATGTTCAAATTATGACATAATTAAATA
1 TATTAATGATGTTCAAATTATGACATAATTAAATA
28196937 ATCAAACTAA
Statistics
Matches: 62, Mismatches: 10, Indels: 2
0.84 0.14 0.03
Matches are distributed among these distances:
38 34 0.55
39 28 0.45
ACGTcount: A:0.45, C:0.10, G:0.08, T:0.38
Consensus pattern (39 bp):
TATTAATGATGTTCAAATTATGACATAATTAAATACTCA
Found at i:28197798 original size:42 final size:42
Alignment explanation
Indices: 28197739--28197837 Score: 153
Period size: 42 Copynumber: 2.4 Consensus size: 42
28197729 CACACGCTCG
** *
28197739 TGTGCCAGGATGTGTACCCTTCGAAATGGCCTTACAGGCCCA
1 TGTGCCAGGCCGTGTACCCTTCGAAATGGCCTTACAGGACCA
*
28197781 TGTGCCAGGCCGTGTACCCTTCGAAATGGCCTTACATGACCA
1 TGTGCCAGGCCGTGTACCCTTCGAAATGGCCTTACAGGACCA
*
28197823 TGTGCTAGGCCGTGT
1 TGTGCCAGGCCGTGT
28197838 GAAGCTACTG
Statistics
Matches: 52, Mismatches: 5, Indels: 0
0.91 0.09 0.00
Matches are distributed among these distances:
42 52 1.00
ACGTcount: A:0.19, C:0.28, G:0.27, T:0.25
Consensus pattern (42 bp):
TGTGCCAGGCCGTGTACCCTTCGAAATGGCCTTACAGGACCA
Found at i:28210985 original size:46 final size:44
Alignment explanation
Indices: 28210960--28211198 Score: 219
Period size: 46 Copynumber: 5.5 Consensus size: 44
28210950 GATCAAGTGA
* ** *
28210960 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGAT
1 CAAGTGACAAGTGATAAGTGATAG-TTTAGCTACACTTATCTGAT
* *
28211005 CAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAG-TTTAGCTACACTTATCTGAT
*
28211051 CAAGTG--AA---A-AAGTGATAAG--T-GCTATACTTATCTGAT
1 CAAGTGACAAGTGATAAGTGAT-AGTTTAGCTACACTTATCTGAT
* *
28211087 CAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGAT
1 CAAGTGAC-AAGTGATAAGTGATAG-TTTAGCTACACTTATCTGAT
* * **
28211133 CAAGTGAGAAAGTGATAAGTGGTAGCCTAGCTACACTTATCTGAT
1 CAAGTGA-CAAGTGATAAGTGATAGTTTAGCTACACTTATCTGAT
*
28211178 C-AGGGACAAGTGATAAGTGAT
1 CAAGTGACAAGTGATAAGTGAT
28211199 CATATGTAAG
Statistics
Matches: 163, Mismatches: 17, Indels: 30
0.78 0.08 0.14
Matches are distributed among these distances:
36 21 0.13
37 1 0.01
39 8 0.05
40 3 0.02
42 3 0.02
43 21 0.13
44 4 0.02
45 27 0.17
46 75 0.46
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (44 bp):
CAAGTGACAAGTGATAAGTGATAGTTTAGCTACACTTATCTGAT
Found at i:28210986 original size:52 final size:52
Alignment explanation
Indices: 28210907--28211071 Score: 198
Period size: 52 Copynumber: 3.2 Consensus size: 52
28210897 TACTTCTGAT
*
28210907 CAAGTGACAAAGCGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
1 CAAGTGA-AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
* ** * *
28210960 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGA
1 CAAGTGAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
28211012 C------AAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGAA
1 CAAGTGAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTG-A
* *
28211059 AAAGTGATAAGTG
1 CAAGTGAAAAGTG
28211072 CTATACTTAT
Statistics
Matches: 92, Mismatches: 13, Indels: 14
0.77 0.11 0.12
Matches are distributed among these distances:
46 39 0.42
47 1 0.01
52 40 0.43
53 12 0.13
ACGTcount: A:0.36, C:0.14, G:0.23, T:0.27
Consensus pattern (52 bp):
CAAGTGAAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAAGTGA
Found at i:28211081 original size:36 final size:36
Alignment explanation
Indices: 28211035--28211107 Score: 128
Period size: 36 Copynumber: 2.0 Consensus size: 36
28211025 GGTAGCTTTA
28211035 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
* *
28211071 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGT
1 GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
28211107 G
1 G
28211108 TTAGCCTTAG
Statistics
Matches: 35, Mismatches: 2, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
36 35 1.00
ACGTcount: A:0.37, C:0.14, G:0.21, T:0.29
Consensus pattern (36 bp):
GCTACACTTATCTGATCAAGTGAAAAAGTGATAAGT
Found at i:28211126 original size:82 final size:82
Alignment explanation
Indices: 28210989--28211153 Score: 294
Period size: 82 Copynumber: 2.0 Consensus size: 82
28210979 GATAGCTTCG
*
28210989 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCTTTAGCTACACTTATCTGATCAA
1 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
28211054 GTGAAAAAGTGATAAGT
66 GTGAAAAAGTGATAAGT
* *
28211071 GCTATACTTATCTGATCAAGTGACAAAGTGATAAGTGTTAGCCTTAGCTACACTTATCTGATCAA
1 GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
*
28211136 GTGAGAAAGTGATAAGT
66 GTGAAAAAGTGATAAGT
28211153 G
1 G
28211154 GTAGCCTAGC
Statistics
Matches: 79, Mismatches: 4, Indels: 0
0.95 0.05 0.00
Matches are distributed among these distances:
82 79 1.00
ACGTcount: A:0.35, C:0.14, G:0.21, T:0.30
Consensus pattern (82 bp):
GCTATACTTATCTGATCAAGAGACAAAGTGATAAGTGGTAGCCTTAGCTACACTTATCTGATCAA
GTGAAAAAGTGATAAGT
Found at i:28211134 original size:128 final size:124
Alignment explanation
Indices: 28210960--28211196 Score: 350
Period size: 128 Copynumber: 1.9 Consensus size: 124
28210950 GATCAAGTGA
* *
28210960 CAAGTGAAAAGTGATAAGTGATAGCTTCGGCTATACTTATCTGATCAAGAGACAAAGTGATAAGT
1 CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
*
28211025 GGTAGCTTTAGCTACACTTATCTGATCAAGTGAAAAAGTGATAAGTGCTATACTTATCTGAT
66 GGTAGC-CTAGCTACACTTATCTGATC-AG-GAAAAAGTGATAAGTGCTATACTTATCTGAT
* * *
28211087 CAAGTGACAAAGTGATAAGTGTTAGCCTT-AGCTACACTTATCTGATCAAGTGAGAAAGTGATAA
1 CAAGTGA-AAAGTGATAAGTGATAG-CTTCAGCTACACTTATCTGATCAAGAGACAAAGTGATAA
* *
28211151 GTGGTAGCCTAGCTACACTTATCTGATCAGGGACAAGTGATAAGTG
64 GTGGTAGCCTAGCTACACTTATCTGATCAGGAAAAAGTGATAAGTG
28211197 ATCATATGTA
Statistics
Matches: 100, Mismatches: 8, Indels: 6
0.88 0.07 0.05
Matches are distributed among these distances:
125 14 0.14
126 2 0.02
127 26 0.26
128 55 0.55
129 3 0.03
ACGTcount: A:0.35, C:0.14, G:0.23, T:0.28
Consensus pattern (124 bp):
CAAGTGAAAAGTGATAAGTGATAGCTTCAGCTACACTTATCTGATCAAGAGACAAAGTGATAAGT
GGTAGCCTAGCTACACTTATCTGATCAGGAAAAAGTGATAAGTGCTATACTTATCTGAT
Found at i:28214227 original size:27 final size:27
Alignment explanation
Indices: 28214189--28214278 Score: 112
Period size: 27 Copynumber: 3.3 Consensus size: 27
28214179 TGGAGGGTTT
*
28214189 CTGATTGGCGGCACCAAAGGTGCCATA
1 CTGATTGGCGGCACCAATGGTGCCATA
*
28214216 CTGATTGGCGGCACCGATGGTGCCA-A
1 CTGATTGGCGGCACCAATGGTGCCATA
* *
28214242 -TGAGGTTGGCAGCACCAATGGTTCCATA
1 CTGA--TTGGCGGCACCAATGGTGCCATA
28214270 CTGATTGGC
1 CTGATTGGC
28214279 AGGACTACTC
Statistics
Matches: 54, Mismatches: 5, Indels: 8
0.81 0.07 0.12
Matches are distributed among these distances:
25 3 0.06
26 1 0.02
27 46 0.85
28 1 0.02
29 3 0.06
ACGTcount: A:0.22, C:0.24, G:0.31, T:0.22
Consensus pattern (27 bp):
CTGATTGGCGGCACCAATGGTGCCATA
Found at i:28214380 original size:10 final size:10
Alignment explanation
Indices: 28214365--28214403 Score: 51
Period size: 10 Copynumber: 3.8 Consensus size: 10
28214355 AGGTGCTGCG
28214365 GAAAAAAAGA
1 GAAAAAAAGA
*
28214375 GAAAAAGAGA
1 GAAAAAAAGA
*
28214385 GAAAGAGAAGA
1 GAAA-AAAAGA
28214396 GAAAAAAA
1 GAAAAAAA
28214404 AGGTATTTTT
Statistics
Matches: 24, Mismatches: 4, Indels: 2
0.80 0.13 0.07
Matches are distributed among these distances:
10 16 0.67
11 8 0.33
ACGTcount: A:0.74, C:0.00, G:0.26, T:0.00
Consensus pattern (10 bp):
GAAAAAAAGA
Found at i:28214531 original size:3 final size:3
Alignment explanation
Indices: 28214523--28214547 Score: 50
Period size: 3 Copynumber: 8.3 Consensus size: 3
28214513 TTTTAGCTAG
28214523 TAT TAT TAT TAT TAT TAT TAT TAT T
1 TAT TAT TAT TAT TAT TAT TAT TAT T
28214548 GTTGTTGTTG
Statistics
Matches: 22, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 22 1.00
ACGTcount: A:0.32, C:0.00, G:0.00, T:0.68
Consensus pattern (3 bp):
TAT
Found at i:28214552 original size:3 final size:3
Alignment explanation
Indices: 28214546--28214604 Score: 118
Period size: 3 Copynumber: 19.7 Consensus size: 3
28214536 ATTATTATTA
28214546 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
1 TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG TTG
28214594 TTG TTG TTG TT
1 TTG TTG TTG TT
28214605 CTTAGTATTA
Statistics
Matches: 56, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
3 56 1.00
ACGTcount: A:0.00, C:0.00, G:0.32, T:0.68
Consensus pattern (3 bp):
TTG
Found at i:28214759 original size:140 final size:140
Alignment explanation
Indices: 28214604--28214884 Score: 562
Period size: 140 Copynumber: 2.0 Consensus size: 140
28214594 TTGTTGTTGT
28214604 TCTTAGTATTAAGATGTTATTAAGGTATTAAGATGTTACTTAGTATTATTGTTAGTAAAAAACTA
1 TCTTAGTATTAAGATGTTATTAAGGTATTAAGATGTTACTTAGTATTATTGTTAGTAAAAAACTA
28214669 GTATTATTATTATGGTTAGTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAACTAGT
66 GTATTATTATTATGGTTAGTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAACTAGT
28214734 ATTATTATTA
131 ATTATTATTA
28214744 TCTTAGTATTAAGATGTTATTAAGGTATTAAGATGTTACTTAGTATTATTGTTAGTAAAAAACTA
1 TCTTAGTATTAAGATGTTATTAAGGTATTAAGATGTTACTTAGTATTATTGTTAGTAAAAAACTA
28214809 GTATTATTATTATGGTTAGTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAACTAGT
66 GTATTATTATTATGGTTAGTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAACTAGT
28214874 ATTATTATTA
131 ATTATTATTA
28214884 T
1 T
28214885 AGTTAGTTAG
Statistics
Matches: 141, Mismatches: 0, Indels: 0
1.00 0.00 0.00
Matches are distributed among these distances:
140 141 1.00
ACGTcount: A:0.38, C:0.05, G:0.12, T:0.45
Consensus pattern (140 bp):
TCTTAGTATTAAGATGTTATTAAGGTATTAAGATGTTACTTAGTATTATTGTTAGTAAAAAACTA
GTATTATTATTATGGTTAGTTATTATTTTTATTTACCAAAATAAACTAGTTAGTAAAAAACTAGT
ATTATTATTA
Found at i:28220100 original size:154 final size:159
Alignment explanation
Indices: 28219858--28220324 Score: 493
Period size: 154 Copynumber: 3.0 Consensus size: 159
28219848 GTAATACACT
* * *
28219858 CTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTATTTTAGAAAATATTATAATT
1 CTTACTCCGGCCATTTGCTCGTATTATTTTCTCCGCATTTTATTATTTTAGAAAATA-TATAATT
28219923 TTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTAGTGTGTTT
65 TTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTAGTGTGTTT
28219988 TTTAAATTAATTTGGTGTAAGAAAAAAACC
130 TTTAAATTAATTTGGTGTAAGAAAAAAACC
* *
28220018 CTTA-TCCCTGCCCTTTGCTCGTATTATTTTC-CCG-ATTTTTATT-TCTTTCA-ATAAA-A-AT
1 CTTACT-CCGGCCATTTGCTCGTATTATTTTCTCCGCA-TTTTATTAT-TTT-AGA-AAATATAT
* * * **
28220076 -A-TTTT-ATTTTCTTATTTTATATTATTTCAGTGCATTTTGTTTGAAATATTTGTATTAA-TTA
61 AATTTTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTG-AA-A-TT-TATTAATTTA
* * * * * * * *
28220137 TTTCTGAATTTTTAAA--AA---AGT-T-AGTAATACACT
122 -GTGTG-TTTTTTAAATTAATTTGGTGTAAGAAAAAAACC
* * *
28220170 CTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTATTTTAGAAAATATTATAATT
1 CTTACTCCGGCCATTTGCTCGTATTATTTTCTCCGCATTTTATTATTTTAGAAAATA-TATAATT
*
28220235 TTTAATTTTATAATTTTACATTATTTCAGTGCTTAATGTTTGAAATTTATTAATTTAGTGTGTTT
65 TTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTAGTGTGTTT
28220300 TTTAAATTAATTTGGTGTAAGAAAA
130 TTTAAATTAATTTGGTGTAAGAAAA
28220325 TACATTACTT
Statistics
Matches: 242, Mismatches: 35, Indels: 60
0.72 0.10 0.18
Matches are distributed among these distances:
152 35 0.14
153 25 0.10
154 46 0.19
155 15 0.06
156 4 0.02
157 15 0.06
158 45 0.19
159 25 0.10
160 32 0.13
ACGTcount: A:0.28, C:0.10, G:0.10, T:0.51
Consensus pattern (159 bp):
CTTACTCCGGCCATTTGCTCGTATTATTTTCTCCGCATTTTATTATTTTAGAAAATATATAATTT
TTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTAGTGTGTTTT
TTAAATTAATTTGGTGTAAGAAAAAAACC
Found at i:28220333 original size:158 final size:157
Alignment explanation
Indices: 28219858--28220335 Score: 513
Period size: 158 Copynumber: 3.1 Consensus size: 157
28219848 GTAATACACT
28219858 CTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTATTTTAGAAAATATTATAATT
1 CTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTATTTTAGAAAATATTATAATT
*
28219923 TTTAATTTTATAATTTTACATTATTTCAGTGCATAATGTTTGAAATTTATTAATTTAGTGTGTTT
66 TTTAATTTTATAATTTTACATTATTTCAGTGCTTAATGTTTGAAATTTATTAATTTAGTGTGTTT
*
28219988 TTTAAATTAATTTGGTGTAAGAAAAAAA
131 TTTAAATTAATTTGGTGTAAG-AAAATA
* * * * *
28220016 CCCTTA-TCCCTGCCCTTTGCTCGTATTATTTTC-CCG-ATTTTTATT-TCTTTCA-ATAAA-A-
1 --CTTACT-TCGGCCATTTGTTCGTATTTTTTTCTCCGCA-TTTTATTAT-TTT-AGA-AAATAT
* * * *
28220074 -AT-A-TTTT-ATTTTCTTATTTTATATTATTTCAGTGCATT-TTGTTTGAAATATTTGTATTAA
59 TATAATTTTTAATTTTATAATTTTACATTATTTCAGTGC-TTAATGTTTG-AA-A-TT-TATTAA
* * * * * * * * *
28220134 -TTATTTCTGAATTTTTAAA-AAAGTT--AGTAATACACT-
119 TTTA-GTGTG-TTTTTTAAATTAATTTGGTGTAAGAAAATA
28220170 CTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTATTTTAGAAAATATTATAATT
1 CTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTATTTTAGAAAATATTATAATT
28220235 TTTAATTTTATAATTTTACATTATTTCAGTGCTTAATGTTTGAAATTTATTAATTTAGTGTGTTT
66 TTTAATTTTATAATTTTACATTATTTCAGTGCTTAATGTTTGAAATTTATTAATTTAGTGTGTTT
28220300 TTTAAATTAATTTGGTGTAAGAAAATA
131 TTTAAATTAATTTGGTGTAAGAAAATA
28220327 CATTACTTC
1 C-TTACTTC
28220336 AGTGCATTAT
Statistics
Matches: 250, Mismatches: 38, Indels: 62
0.71 0.11 0.18
Matches are distributed among these distances:
152 28 0.11
153 24 0.10
154 46 0.18
155 16 0.06
156 15 0.06
157 16 0.06
158 53 0.21
159 24 0.10
160 28 0.11
ACGTcount: A:0.28, C:0.11, G:0.10, T:0.51
Consensus pattern (157 bp):
CTTACTTCGGCCATTTGTTCGTATTTTTTTCTCCGCATTTTATTATTTTAGAAAATATTATAATT
TTTAATTTTATAATTTTACATTATTTCAGTGCTTAATGTTTGAAATTTATTAATTTAGTGTGTTT
TTTAAATTAATTTGGTGTAAGAAAATA
Found at i:28220727 original size:24 final size:24
Alignment explanation
Indices: 28220700--28220762 Score: 89
Period size: 23 Copynumber: 2.8 Consensus size: 24
28220690 TATTTTTTTC
28220700 TTTTTTTTC-C-T-TCCTTCCCTT
1 TTTTTTTTCTCTTCTCCTTCCCTT
*
28220721 TTTTTTTTCTCTTCTCCTTTCC-T
1 TTTTTTTTCTCTTCTCCTTCCCTT
28220744 TTTTTTTTCTCTTCTCCTT
1 TTTTTTTTCTCTTCTCCTT
28220763 TCTTTTTCTT
Statistics
Matches: 38, Mismatches: 1, Indels: 4
0.88 0.02 0.09
Matches are distributed among these distances:
21 9 0.24
22 1 0.03
23 21 0.55
24 7 0.18
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (24 bp):
TTTTTTTTCTCTTCTCCTTCCCTT
Found at i:28220734 original size:18 final size:19
Alignment explanation
Indices: 28220699--28220769 Score: 65
Period size: 23 Copynumber: 3.5 Consensus size: 19
28220689 TTATTTTTTT
28220699 CTTTTTTTTCCTTC-CTTC-C
1 CTTTTTTTT--TTCTCTTCTC
28220718 CTTTTTTTTTTCTCTTCTC
1 CTTTTTTTTTTCTCTTCTC
28220737 CTTTCCTTTTTTTTTCTCTTCTC
1 C--T--TTTTTTTTTCTCTTCTC
28220760 CTTTCTTTTT
1 CTTT-TTTTT
28220770 CTTTCCTTCT
Statistics
Matches: 45, Mismatches: 0, Indels: 13
0.78 0.00 0.22
Matches are distributed among these distances:
17 3 0.07
18 4 0.09
19 13 0.29
20 5 0.11
21 2 0.04
23 18 0.40
ACGTcount: A:0.00, C:0.30, G:0.00, T:0.70
Consensus pattern (19 bp):
CTTTTTTTTTTCTCTTCTC
Found at i:28220769 original size:41 final size:39
Alignment explanation
Indices: 28220725--28220849 Score: 143
Period size: 36 Copynumber: 3.3 Consensus size: 39
28220715 TCCCTTTTTT
* *
28220725 TTTTCTCTTCTCCTTTCCTTTTTTTTTCTCTTCTCCTTTC
1 TTTT-TCTTCTCCTTTCCTTTTTTTTTCTCTTTTTCTTTC
*
28220765 TTTTTCTT-TCC-TT-CTTTTTCTTTCT-TTTTTC-TTC
1 TTTTTCTTCTCCTTTCCTTTTTTTTTCTCTTTTTCTTTC
* *
28220799 TTTTTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTC
1 TTTTTCTTCTCCTTTCCTTTTTTTTTC-TCTTTTTCTTTC
28220839 ATTTTTCTTCT
1 -TTTTTCTTCT
28220850 TCTTCTTCTT
Statistics
Matches: 72, Mismatches: 6, Indels: 13
0.79 0.07 0.14
Matches are distributed among these distances:
34 11 0.15
35 7 0.10
36 13 0.18
37 10 0.14
38 4 0.06
39 10 0.14
40 7 0.10
41 10 0.14
ACGTcount: A:0.01, C:0.28, G:0.00, T:0.71
Consensus pattern (39 bp):
TTTTTCTTCTCCTTTCCTTTTTTTTTCTCTTTTTCTTTC
Found at i:28220773 original size:10 final size:10
Alignment explanation
Indices: 28220742--28220929 Score: 111
Period size: 10 Copynumber: 18.8 Consensus size: 10
28220732 TTCTCCTTTC
*
28220742 CTTTTTTTTT
1 CTTTCTTTTT
*
28220752 CTCTTCTCCTTT
1 CT-TTCT-TTTT
28220764 CTTT-TTCTTT
1 CTTTCTT-TTT
*
28220774 CCTTCTTTTT
1 CTTTCTTTTT
28220784 CTTTCTTTTT
1 CTTTCTTTTT
28220794 -TCTTCTTTTT
1 CT-TTCTTTTT
* *
28220804 CTTCTCCTTTC
1 CTT-TCTTTTT
*
28220815 CTTT-TCTTT
1 CTTTCTTTTT
*
28220824 CCTTCTTTTT
1 CTTTCTTTTT
28220834 CTTTCATTTTT
1 CTTTC-TTTTT
*
28220845 C-TTCTTCTT
1 CTTTCTTTTT
* *
28220854 C-TTCTTCTC
1 CTTTCTTTTT
* *
28220863 CTTTCCTTTC
1 CTTTCTTTTT
*
28220873 CTTTCCTTTT
1 CTTTCTTTTT
28220883 C-TTCTTTTT
1 CTTTCTTTTT
* * *
28220892 CTTTCCTCTC
1 CTTTCTTTTT
*
28220902 CTTTCCTTTT
1 CTTTCTTTTT
28220912 CTTTCTTTCTT
1 CTTTCTTT-TT
28220923 C-TTCTTT
1 CTTTCTTT
28220930 CCCTCTCTTC
Statistics
Matches: 141, Mismatches: 25, Indels: 24
0.74 0.13 0.13
Matches are distributed among these distances:
9 27 0.19
10 84 0.60
11 25 0.18
12 5 0.04
ACGTcount: A:0.01, C:0.30, G:0.00, T:0.70
Consensus pattern (10 bp):
CTTTCTTTTT
Found at i:28220803 original size:53 final size:52
Alignment explanation
Indices: 28220747--28220889 Score: 211
Period size: 50 Copynumber: 2.8 Consensus size: 52
28220737 CTTTCCTTTT
* *
28220747 TTTTTCTCTTCTCCTTTCTTTTTCTTTCCTTCTTTTTCTTTCTTTTTTCTTC
1 TTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCATTTTTCTTC
28220799 -TTTT-TCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCATTTTTCTTC
1 TTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCATTTTTCTTC
* * *
28220849 TTCTTCTTCTTCTCCTTTCCTTTCCTTTCCTT-TTCTTCTTT
1 TTTTTC-TCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTT
28220890 TTCTTTCCTC
Statistics
Matches: 83, Mismatches: 5, Indels: 6
0.88 0.05 0.06
Matches are distributed among these distances:
50 44 0.53
51 7 0.08
52 8 0.10
53 24 0.29
ACGTcount: A:0.01, C:0.29, G:0.00, T:0.70
Consensus pattern (52 bp):
TTTTTCTCTTCTCCTTTCCTTTTCTTTCCTTCTTTTTCTTTCATTTTTCTTC
Found at i:28220860 original size:6 final size:6
Alignment explanation
Indices: 28220762--28220861 Score: 50
Period size: 6 Copynumber: 17.2 Consensus size: 6
28220752 CTCTTCTCCT
* * * *
28220762 TTCTTT TTCTT- TCCTTC TTTTTC TTTCTT- TT-TTC TTCTTT TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC -TTCTTC TTCTTC TTCTTC TTCTTC
* * * * *
28220808 TCCTT- TCCTT- TTCTT- TCCTTC TTTTTC TTTCATTT TTCTTC TTCTTC
1 TTCTTC TTCTTC TTCTTC TTCTTC TTCTTC -TTC-TTC TTCTTC TTCTTC
28220855 TTCTTC T
1 TTCTTC T
28220862 CCTTTCCTTT
Statistics
Matches: 73, Mismatches: 14, Indels: 14
0.72 0.14 0.14
Matches are distributed among these distances:
4 2 0.03
5 21 0.29
6 39 0.53
7 9 0.12
8 2 0.03
ACGTcount: A:0.01, C:0.27, G:0.00, T:0.72
Consensus pattern (6 bp):
TTCTTC
Found at i:28220871 original size:5 final size:5
Alignment explanation
Indices: 28220861--28220920 Score: 61
Period size: 5 Copynumber: 12.4 Consensus size: 5
28220851 CTTCTTCTTC
* * * *
28220861 TCCTT TCCTT TCCTT TCCTT TTC-T TCTTT TTCTT TCCTC TCCTT TCCTT
1 TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT TCCTT
*
28220910 TTCTT T-CTT TC
1 TCCTT TCCTT TC
28220921 TTCTTCTTTC
Statistics
Matches: 44, Mismatches: 9, Indels: 4
0.77 0.16 0.07
Matches are distributed among these distances:
4 6 0.14
5 38 0.86
ACGTcount: A:0.00, C:0.35, G:0.00, T:0.65
Consensus pattern (5 bp):
TCCTT
Done.